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VAT Refunds and Tax Credits Guide

- MPC claimed a VAT refund of PHP 148 million, which included PHP 136 million from Official Receipt 0189 for purchases from 1993-1996. - The BIR Commissioner denied the claim, finding OR 0189 doubtful since it was dated 1998 but covered 1993-1996 purchases. Further, most claims had prescribed. - The Court partially granted the petition. It relied on an SGV audit finding PHP 10.7 million supported. It denied the OR 0189 amount since VAT invoices/receipts are best evidence, and denied the remaining claims as prescribed.

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0% found this document useful (0 votes)

284 views42 pages

VAT Refunds and Tax Credits Guide

Uploaded by

Jesús Lapuz

We take content rights seriously. If you suspect this is your content, claim it here.

Available Formats

Download as DOC, PDF, TXT or read online on Scribd

MONTERO // 3A TAX DIGESTS

AGATEP ALARCON ARCAINA AUSTRIA BAADERA BANTA BELLO BUGAY CARAAN COLOQUIO CUALOPING DE LUIS DIPLOMA FAJARDO GO GUZMAN
LAYNO LIM, J. LIM, Q. LUNA OCAMPO ONG PASCUAL REYES ROCILLO TRIAS TUAZON VANSLEMBROUCK VILLARIN, L. VILLARIN, P. VILLARIVERA

VAT REFUNDS

Made. - In proper cases, the Commissioner shall grant a refund or issue

the tax credit certificate for creditable input taxes within one hundred

SECTION 112. Refunds or Tax Credits of Input Tax.

twenty (120) days from the date of submission of complete documents in

(A) Zero-rated or Effectively Zero-rated Sales. - Any VAT-registered

support of the application filed in accordance with Subsections (A) hereof.

person, whose sales are zero-rated or effectively zero-rated may, within

In case of full or partial denial of the claim for tax refund or tax credit, or

two (2) years after the close of the taxable quarter when the sales were

the failure on the part of the Commissioner to act on the application within

made, apply for the issuance of a tax credit certificate or refund of

the period prescribed above, the taxpayer affected may, within thirty (30)

creditable input tax due or paid attributable to such sales, except

days from the receipt of the decision denying the claim or after the

transitional input tax, to the extent that such input tax has not been applied

expiration of the one hundred twenty day-period, appeal the decision or

against output tax: Provided, however, That in the case of zero-rated sales

the unacted claim with the Court of Tax Appeals.

under Section 106(A)(2)(a)(1), (2) and (b) and Section 108 (B)(1) and (2),
the acceptable foreign currency exchange proceeds thereof had been duly

(D) Manner of Giving Refund. - Refunds shall be made upon warrants

accounted for in accordance with the rules and regulations of the Bangko

drawn by the Commissioner or by his duly authorized representative

Sentral ng Pilipinas (BSP): Provided, further, That where the taxpayer is

without the necessity of being countersigned by the Chairman,

engaged in zero-rated or effectively zero-rated sale and also in taxable or

Commission on audit, the provisions of the Administrative Code of 1987 to

exempt sale of goods of properties or services, and the amount of

the contrary notwithstanding: Provided, That refunds under this paragraph

creditable input tax due or paid cannot be directly and entirely attributed to

shall be subject to post audit by the Commission on Audit.

any one of the transactions, it shall be allocated proportionately on the

basis of the volume of sales. Provided, finally, That for a person making

Section 112. Refunds or Tax Credits of Input Tax. -

sales that are zero-rated under Section 108(B) (6), the input taxes shall be

(A) Zero-rated or Effectively Zero-rated Sales.

allocated ratably between his zero-rated and non-zero-rated sales.

Any VAT-registered person,

(B) Cancellation of VAT Registration. - A person whose registration has

Whose sales are zero-rated or

Effectively zero-rated

been cancelled due to retirement from or cessation of business, or due to

changes in or cessation of status under Section 106(C) of this Code may,
within two (2) years from the date of cancellation, apply for the issuance of

May, within two (2) years

a tax credit certificate for any unused input tax which may be used in

After the close of the taxable quarter when the sales were
made,

payment of his other internal revenue taxes.

Apply for the issuance of a
(C) Period within which Refund or Tax Credit of Input Taxes shall be

Tax credit certificate or

MONTERO // 3A TAX DIGESTS

Refund of creditable input tax

Due or paid attributable to such sales,

May, within two (2) years from the date of cancellation,

Apply for the issuance of a tax credit certificate

Except transitional input tax,

For any unused input tax which may be used in

payment of his other internal revenue taxes.

To the extent that such input tax has not been

applied against output tax:

Provided, however, that in the case of zero-rated sales under Section 106(A)
(2)(a)(1), (2) and (b) and Section 108 (B)(1) and (2),

In proper cases, the Commissioner shall

The acceptable foreign currency exchange proceeds thereof

Had been duly accounted for in accordance with the rules

Grant a refund or

Issue the tax credit certificate

and regulations of the Bangko Sentral ng Pilipinas (BSP):

Provided, further, that where the taxpayer is

Engaged in zero-rated or effectively zero-rated sale AND ALSO

In taxable or exempt sale of goods of properties or services, AND

The amount of creditable input tax due or paid cannot be directly

and entirely attributed to any one of the transactions,

It shall be allocated proportionately on the basis of the volume of sales.

For creditable input taxes within one hundred twenty

(120) days from the date of submission of complete
documents in support of the application filed

In accordance with Subsections (A) hereof.

In case of

Provided, finally,

Full or partial denial of the claim for tax refund or tax credit, or
The failure on the part of the Commissioner to act on the
application within the period prescribed above,

That for a person making sales that are zero-rated under Section 108(B) (6),

The input taxes shall be allocated ratably between his zero-rated

and non-zero-rated sales.

The taxpayer affected may,

Within thirty (30) days from the receipt of the decision denying the
claim or

(B) Cancellation of VAT Registration.

A person whose registration

Has been cancelled due to retirement from or

Cessation of business, or

Due to changes in or cessation of status under Section 106(C) of

this Code

After the expiration of the one hundred twenty day-period,

Appeal the decision or the unacted claim with the Court of Tax Appeals.
(D) Manner of Giving Refund.
Refunds shall be made upon warrants

Drawn by the Commissioner or

MONTERO // 3A TAX DIGESTS

By his duly authorized representative

Mitsubishi. On Aug 25, 1998 when MPC filed its 2 nd quarter tax
return, it stated an input VAT of PhP 148,003,047.62, which included

Without the necessity of being countersigned by

PhP 135,993,570 supported by OR No. 0189. On December 20,

The Chairman,

1999 it filed for an administrative claim for refund for unutilized input

Commission on audit,

VAT for the amount of P148,003,047.62. BIR Commissioner did not

grant his claim as these were not supported by documents. With

The provisions of the Administrative Code of 1987 to the contrary

regard to OR No. 0189, it is of doubtful veracity as it is dated at 1998

notwithstanding:

but pertains to purchases rendered for the years 1993 to 1996. It

Provided, that refunds under this paragraph

shall also be denied for the reason that it has prescribed from the 2

Shall be subject to post audit by the Commission on Audit.

year period to claim for refund from the date of purchase.

CIR v. MIRANT (Alarcon)

Issue: WON MPC can claim for creditable VAT refund for the amount of

[GR. No. 172129; September 12, 2008]

P148, 003, 047.62? No, only P10, 733, 969

BIR Rulings overturned; Peace bonds are deposit substitutes

Held:

No. Petition Partly granted. CTA employed the services of SGV and

Recit-Ready:

findings of such firm with regard to the amounts unsupported by

Facts: MPC is engaged in generation of power which it sells to National

documentary evidence shall be relied upon. With regard to the

Power Corportaion (NPC). Under Sec 13 of RA 6935, NPC is

amount supported by OR No. 0189, Sec 110 of the NIRC provides

exempt from all taxes, direct or indirect. Upon the belief that its sale

that the a VAT invoice or an Official Receipt is the best evidence to

to NPC of power was zero rated for tax purposes, MPC applied for

prove such payment of VAT. However, the petition should be denied

effective zero rating for the Build, Operate, Transfer scheme of its

as the claim for refund has prescribed. The prescription period for

Pagbilao Power station. MPC acquired goods and services from

claims of refund are to be reckoned from the end of the quarter from

Mitsubishi Japan for the construction of its plant amounting to P

where the purchases were made and not when such tax was

135,993,570 for the years 1993-1996. With its belief to be zero-

actually paid as claim by MPC, as such tax was not erroneously

rated, it opted not to pay the VAT component of its billings from

paid.

Mitsubishi. This caused Mitsubishi to advance payments for the VAT

components as this serves as their output VAT which is essential in
the determination of their VAT payments. It was only on April 14,

Facts:

Mirant Pagbilao Corporation (MPC) is domestic firm engaged in the

1998 that MPC paid Mitsubishi for its VAT component for purchases

generation of power which it sells to National Power Corporation

for 1993-1996, such was evidenced by OR No. 0189 issued by

(NPC).

MONTERO // 3A TAX DIGESTS

MPC was formerly Southern Energy Quezon, Inc. and also

VAT component of the progress billings from Mitsubishi for the

formerly Hopewell (Phil.)Corp

For the construction of its electrical and mechanical equipment

period covering April 1993 to September 1996for the E & M

Equipment Erection Portion of MPCs contract with Mitsubishi.

o This prompted Mitsubishi to advance the VAT component

portion of its Pagbilao, Quezon plant from the years1993-1996, MPC

exempt from all taxes.

o In Maceda v Macaraig, it was ruled that this exemption

as this serves as its output VAT which is essential for the

secured the services of Mitsubishi Corporation (Mitsubishi) of Japan.

Under Section 13 of RA 6935, the revised charter of NPC, NPC is

component for the progress billings from April 1993 to September

covered both direct and indirect taxes.

MPC on the belief that its sale of power generation services to NPC
is, pursuant to Sec. 108(B)(3) of the Tax Code, 1 zero-rated for VAT
purposes, filed on December 1, 1997 with Revenue District Office

1996, and for which Mitsubishi issued Official Receipt (OR) No.

reflected an input VAT of PhP 148,003,047.62, which included

Rating.
o This application covered the construction and operation of

PhP 135,993,570 supported by OR No. 0189.

o Pursuant to procedure in RR-7-95, MPC filed on December

its Pagbilao power station under a Build, Operate, and

application in the form of a request for ruling with the VAT Review

20, 1999 an administrative claim for refund of unutilized

under Sec. 229 of the National Internal Revenue Code (NIRC), MPC
went to the CTA via a petition for review, docketed as CTA Case No.

052-99 stating that the supply of electricity by Hopewell

6133.
o

Phil. (MPC) to the NPC, shall be subject to the zero percent

(0%) VAT, pursuant to Section 108 (B) (3) of the National

Philippines by VAT-registered persons shall be subject to zero- percent rate: x x x (3)

Services rendered to persons whose exemption under special laws x x x effectively subjects
the supply of such services to zero percent (0%) rate.

Answering the petition, BIR Commissioner citing KumaiGumi Co. Ltd. V CIR asserted that MPCs claim for refund

Internal Revenue Code of 1997.

Consistent with its belief to be zero-rated, MPC opted not to pay the

Transactions Subject to Zero Percent (%) [Link] following services performed in the

input VAT in the amount of PhP 148,003,047.62.

BIR Commissioner failed to act on its claim for refund (MPC) and
obviously to forestall the running of the two-year prescriptive period

Committee at the BIR national office on January 28, 1999.

o May 13, 1999, CIR Commissioner issued VAT Ruling No.

0189 in the aggregate amount of PhP 135,993,570.

On August 25, 1998, MPC, while awaiting approval of its application,
filed its quarterly VAT return for the second quarter of 1998 where it

(RDO) No. 60 in Lucena City an Application for Effective Zero

Transfer scheme.
Not getting any response from the BIR district office, MPC refiled its

determination of its VAT payment.

It was only on April 14, 1998 that MPC paid Mitsubishi the VAT

cannot be granted for this main reason: MPCs sale of

electricity to NPC is not zero-rated for its failure to secure

an approved application for zero-rating.

March 18, 2003- Court of Tax Appeals granted MPCs claim for input
VAT refund or credit, but only for the amount of PhP
10,766,939.48.
o To provide support to the CTA in verifying and analyzing

MONTERO // 3A TAX DIGESTS

documents and figures and entries contained therein, the

Mitsubishi (Manila) when the invoices which the VAT were

Sycip Gorres & Velayo (SGV), an independent auditing firm,

originally billed came from Mitsubishi Japan.

was commissioned.

Exchange rate in OR No. 0189 was pegged at P26.203=$1

or the exchange rate in 1993 to 1996, when on April 14,
1998, the date when OR No. 0189 was issued, the rate was
already P38 to $1

MPC failed to present its VAT returns for 2 nd and 3rd quarter
of 1995, when such was necessary to determine whether
the amount in OR No. 0189 was not previously refunded or
credited;

No other documents proving the said input VAT payment

were presented other than OR No. 0189

CTA: We agree with the above SGV findings that out of the
remaining taxes of P136,246,017.45, the amount of
P252,477.45 was not supported by any document and
should therefore be outrightly disallowed.
o As to the claimed input tax of P135,993,570.00
(P136,246,017.45 less P252,477.45) on purchases
of services from Mitsubishi Corpora- tion, Japan,

BIR Commissioner argues against the sufficiency of OR No. 0189 to

the same is found to be of doubtful veracity.

prove unutilized input payment by MPC. He states that BIR can

While it is true that said amount is substantiated

require additional evidence to prove and ascertain payment of

by a VAT official receipt with Serial No. 0189

credible input VAT, or that the claim was filed on time or not

dated April 14, 1998 x x x, it must be observed,

previously refunded:

however, that said VAT allegedly paid pertains

OR No. 0189 covers purchases from MPC to Mitsubishi

to the services which were rendered for the

from 1993 to 1996 however MPCs claim for refund was

period 1993 to 1996. x x x

filed on Dec 20, 1999, clearly way beyond the 2 year

prescriptive period in Sec 112 of NIRC
2.

MPC failed to explain why OR No. 0189 was issued by

CA rendered its assailed decision modifying that of the CTA decision

by granting most of MPCs claims for tax refund or credit.

MONTERO // 3A TAX DIGESTS

CA agreed with the CTA on MPCs entitlement to :

(1) a zero- rating for VAT purposes for its sales and

services to tax-exempt NPC; and

(2) a refund or tax credit for its unutilized input VAT

for the second quarter of 1998.

Their disagreement, however, centered on the issue of
proper documentation, particularly the evidentiary value
of OR No. 0189.
CA upheld the disallowance of PhP 1,242,538.14
representing zero-rated input VAT claims supported
only by photocopies of VAT OR/Invoice, and mere

brokers computations.
CA allowed MPCs

refund

claim

goods

and/or

services

Held/Ratio: Petition partly GRANTED.

1. YES. A claim for tax refund may be based on a statute granting tax
exemption, or, the result of legislative grace, in which case, the claim is to be
construed strictissimi juris against the taxpayer; On the other hand, as in
this case, a tax refund may be predicated on tax refund provisions
allowing a refund of erroneous or excess payment of tax, on which
case it is founded on the principle of solutio indebiti, a basic postulate
that no one should unjustly enrich himself at the expense of another;

from

case.

said

claim

since

the

OR No. 0189 issued only on April 14, 1998 clearly reflects the
belated payment of MPC of input VAT. This is supported by a bank

Mitsubishi supported by OR No. 0189. CTA erred in

disallowing

A claim for tax refund proper, as here, necessitates only the

preponderance-of-evidence threshold like in any ordinary civil

PhP

135,993,570 representing input VAT payments for

purchases

No.

statement evidencing payment to Mitsubishi Japan with the amount

from

of P135,993, 570 and a May 12, 1995 letter from Mitsubishi where it

Mitsubishi was the best evidence for the

apprised MPC of the advances Mitsubishi made for the VAT

payment of input VAT by MPC to Mitsubishi as

payments, i.e., MPCs creditable input VAT, and for which it was

required under Sec. 110(A)(1)(b) of the NIRC.

must be viewed as conclusive proof of the

holding MPC accountable for interest therefor.

payment of input VAT

used P26.203=$1 exchange rate in OR No. 0189 for the

VAT payments it advanced in 1993-1996

Issues:
1)

Whether or not respondent [MPC] is entitled to the refund of its

presumably paid on April 14, 1998, the date appearing

[PhP] 146,760,509.48.- No, only 10,766,939.48

Whether or not MPC is entitled to a refund or a TCC for the
alleged unutilized input VAT of PhP 135,993,570 covered by OR
No. 0189 which sufficiently proves payment of the input VAT.

While no available records indicate when the actually

payment for creditable input VAT was made, it is

input VAT payments made from 1993 to 1996 amounting to

Based from the letter, it is understandable why Mitsubishi

in OR No. 0189.

Undoubtedly, OR No. 0189 by itself proves payment of MPC of its

creditable input VAT relative to its purchases payment from
Mitsubishi.

MONTERO // 3A TAX DIGESTS

Sec. 110(A)(1)(B) of the NIRC pertinently provides:

against output tax: x x x. (Emphasis ours.)

Section 110. Tax Credits.A. Creditable Input Tax.

Unutilized input Value Added Tax (VAT) payments not otherwise used for any

(1) Any input tax evidenced by a VAT invoice or official

internal revenue tax due the taxpayer must be claimed within two years

receipt issued in accordance with Section 113 hereof on

reckoned from the close of the taxable quarter when the relevant sales were

the following transactions shall be creditable against the

made pertaining to the input Value Added Tax (VAT) regardless of whether

output tax:

said tax was paid or notthe reckoning frame would always be the end

(a) Purchase or importation of goods: xxxx

of the quarter when the pertinent sales or transaction was made,

(b) Purchase of services on which a value-

regardless when the input VAT was paid.

added tax has been actually paid.

MPC cannot avail itself of the provisions of either Sec. 204(C) or 229

The law considers a duly-executed Value Added Tax (VAT) invoice or

of the NIRC which, for the purpose of refund, prescribes a different

Official Receipt referred to in Section 110(A)(1)(B) of the National

starting point for the two-year prescriptive limit for the filing of a claim

Internal Revenue Code as sufficient evidence to support a claim for

therefor.
o Secs. 204(C) and 229 respectively provide: x x x Notably,

input tax credit.

o And any doubt as to what OR No. 0189 was for or tended to

the above provisions also set a two-year prescriptive period,

prove should reasonably be put to rest by the SGV report on

reckoned from date of payment of the tax or penalty, for the

which the CTA notably placed much reliance.

Matter of nonpayment of MPC of the interest demanded by

filing of a claim of refund or tax credit. Notably too, both

Mitsubishi in the letter, does not invalidate the authenticity of

payment or illegal collection of internal revenue taxes.

provisions apply only to instances of erroneous

payment of VAT in OR No. 0189 as the interest is a matter

between MPC and Mitsubishi.
2. No, The claim for refund or tax credit for the creditable input VAT payment

MPCs creditable input VAT not erroneously paid

wholly-tax exempt client, resulting in a zero-rated or

made by MPC embodied in OR No. 0189 was filed beyond the period

effectively zero-rated transaction, does not deprive the

provided by law for such claim.

taxpayer of its right to a refund for any unutilized creditable

Sec. 112(A) of the NIRC pertinently reads:

input VAT, albeit the erroneous, illegal, or wrongful

(A) Zero-rated or Effectively Zero-rated [Link] VAT-registered

payment angle does not enter the equation.

person, whose sales are zero-rated or effectively zero-rated may, within two
(2) years after the close of the taxable quarter when the sales were
made, apply for the issuance of a tax credit certificate or refund of
creditable input tax due or paid attributable to such sales, except
transitional input tax, to the extent that such input tax has not been applied

Fact that the subsequent sale or transaction involves a

Zero-rated transactions generally refer to the export sale

of goods and supply of services. The tax rate is set at
zero. When applied to the tax base, such rate obviously
results in no tax charge- able against the purchaser. The

MONTERO // 3A TAX DIGESTS

seller of such transactions charges no output tax, but

CIR assailed the Decision on 2 grounds and claimed that: (1) the 2-

can claim a refund of or a tax credit certificate for the

year period lapsed on September 29, 2004 because 2004 was a

VAT previously charged by suppliers.

leap year and under the Civil Code, there are 365 days in a year

Should the input taxes result from zero-rated or effectively

and; (2) the judicial claim was premature

zero-rated transactions or from the acquisition of capital

goods, any excess over the output taxes shall instead be

Issue: WON the administrative and judicial claims were filed on time

refunded to the taxpayer or credited against other internal

administrative YES; judicial - PREMATURE

revenue taxes.

Held:

Hence Sec 112 A not Sec 204 (c) and 209 of the NIRC is controlling in this

In ruling for the CIR, the Court said that:

While there is conflict between the Administrative Code (1 year = 12

case, prescriptive period for a claim for refund shall commence from

months) and the Civil Code (1 year = 365 days), what will prevail in

the end of the quarter of the sale of goods or serves and not the date of

this case is the Administrative Code since leap year or not, there will

payment of the tax. MPCs claim for refund is denied for such has

always be 12 months in a year. SO following this, September 30,

prescribed.

2004 is when the prescriptive period expires.

Section 112, and not Section 114 applies as to the reckoning point of

CIR v. AICHI FORGING (Arcaina)

the prescriptive period. (more on this on the detailed digest, please

[GR. No. 184823; October 6, 2010]

check). But Section 112 provides that

Prescriptive period

Counting of prescriptive period begins from sale/transaction and not from

commences from the close of the taxable quarter when the sales

payment of tax.

were made and not from the time the input VAT was paid nor
from the time the official receipt was issued. (so emphasis on

Recit-Ready:
Facts: Aichi Forging Company is engaged in the manufacturing, producing

was prematurely filed because it is mandated under Section 112(D)

and processing of steel and its by-products. It is a registered VAT

that claimant must wait for 120 days within which the CIR will decide

entity. On September 30, 2004, it filed a claim for refund/credit of

on the administrative claim before filing with the CTA. In this case,

input VAT for the period of July 1 September 30, 2002 with the CIR

Aichi violated the provision when it simultaneously filed the

(under Section 112). On the same day, it filed a Petition for Review

administrative and judicial claims.

for the same refund with the CTA division. CIR assailed the CTA
division decision granting the refund. The CTA En Banc affirmed the
refund and said that in fact and in law, Aichi still has until October 25,
2004 (25 days after the close of taxable quarter or from October 25,
2002, applying Section 114).

TRANSACTION, and not payment of tax.

Although the administrative claim was filed on time, the judicial claim

Facts:

MONTERO // 3A TAX DIGESTS

Aichi Forging Company of Asia (Aichi), a Philippine Corporation, is

Taxpayer engaged in sales which are zero-rated or effectively zero-

o
o

rated substantiated so complied with

the taxpayer is VAT-registered substantiated so complied with
the claim must be filed within two years after the close of the taxable

engaged in the manufacturing, producing and processing of steel and its

by-products.
o Its registered as a VAT entity and its products such as close

impression die steel forgings and tool and dies, are registered with

quarter when such sales were made complied with (as per the 2

the BOI.
On September 30, 2004, Aichi filed a claim for refund/credit of input VAT

year prescriptive period since the filing was made on September 30,

for July 1, 2002 to September 30, 2002 (P3,891,123.82) with the CIR. It

is September 30, 2002)

the creditable input tax due or paid must be attributable to such

2004, to be counted from the closing of the period applied for which

filed a Petition for Review with the CTA for the same refund/credit on the

tax has not been applied against the output tax some claims are

rated sales (P131,791,399). And it paid this amount.

For said period, it incurred and paid input VAT amounting to
P3,912,088.14 from purchases and importation attributable to

baseless and not substantiated.

Effectively: CTA Division granted the refund for P3,239,119.25

because Aichi substantially proved that it was entitled to the same.

CIR sought for reconsideration, insisting that the judicial and admin

its zero-rated sales.

BUT it only claimed P3,891,123.82 with the CIR (so theres a

claims were filed beyond the 2-year period, kasi raw leap year yung

difference of around less than P100K)

CIRs side:
o Claim for refund is subject to administrative investigation by the

September 30. He cited Art. 13 of the Civil Code.

o He added that a prior filing of an administrative claim is a

o
o

Bureau
Aichi must prove it paid VAT input taxes for the period
Aichi must prove that its sales are export sales under Sections

106(A)(2)(a) and 108(B)(1).

Must prove that the claim was filed with the 2-year prescriptive

period under Section 229

In an action for refund, the burden of proof is on the taxpayer to
establish its right to refund, and failure to sustain the burden is

sales, except the transitional input tax, to the extent that such input

same date.
Aichis allegations before the CTA:
o From July 1 September 30, 2002: it generated and recorded zeroo

fatal to the claim of refund

o Claims for refund are construed strictly against the claimant.
CTA partially granted the claim for credit, citing Section 112. Why partial
only? Check the following elements for refund:

2004 SO the 2-year period expired on September 29, and not

condition precedent before a judicial claim can be filed.

o This motion for partial reconsideration was denied.
CIR filed petition before the En Banc, and this was likewise denied. It
affirmed the Division Decision but ruled that the reckoning point for the
prescriptive period is 25 days after the close of each taxable
quarter. (In this case, October 25, 2002 is the reckoning point so the
filing of a claim prescribes on October 25, 2004) This is based from
Section 114.

Issue:
Whether Aichi Forgings judicial and administrative claims were filed
within the 2-year prescriptive period provided in Sections 112(A) and

MONTERO // 3A TAX DIGESTS

229 of the NIRC for administrative claim, YES; but judicial claim was

o Applying such in the case at hand, the 2-year period to file for a tax

PREMATURE.

refund/credit for the July 1-September 30, 2002 period expired on

September 30, 2004.

Held/Ratio: Petition GRANTED. The assailed July 30, 2008 Decision and
the October 6, 2008 Resolution of the Court of Tax Appeals are hereby

3) Judicial claim PREMATURE. Aichi filed in violation of Section

REVERSED and SET ASIDE. The Court of Tax Appeals Second Division is

112(D)

DIRECTED to dismiss CTA Case No. 7065 for having been prematurely filed.

simultaneously.
o

when

filed

its

administrative

and

judicial

claims

SEC. 112. Refunds or Tax Credits of Input Tax. x x x x (D) Period

1) First, Section 112 (A) and NOT Section 114 is the applicable

within which Refund or Tax Credit of Input Taxes shall be [Link]

provision in determining the start of the 2-year period for claiming a

proper cases, the Commissioner shall grant a refund or issue the tax

refund/credit of unutilized input VAT. Court reiterates Mirant ruling.

4. That Section 204(C) and 229 are inapplicable as both provisions

credit certificate for creditable input taxes submission of complete

apply only to instances of erroneous payment or illegal collection of

Subsections (A) and (B) hereof. In case of full or partial denial of

documents in support of the application filed in accordance with

internal revenue taxes.

SEC 112(A): Prescriptive period commences from the close of the

the claim for tax refund or tax credit, or the failure on the part of
the Commissioner to act on the application within the period

taxable quarter when the sales were made and not from the time the
6.

prescribed above, the taxpayer affected may, within thirty (30)

input VAT was paid nor from the time the official receipt was issued.
Thus, when a zero-rated VAT taxpayer pays its input VAT a year after

days from the receipt of the decision denying the claim or after
the expiration of the one hundred twenty day-period, appeal the

the pertinent transaction, said taxpayer only has a year to file a

claim for refund or tax credit of the unutilized creditable input
VAT. So reckoning frame is: end of the quarter when the

lapse of the 120-day period because it filed the claims

pertinent sales or transaction was made, regardless when the

input VAT was paid.
2) Admin claim TIMELY FILED. The Administrative Code which
provides that a year is composed of 12 calendar months, must
prevail over the Civil Code which provides that a year is 365 days.
(Primetown Property Group case)
o Under this case, it was ruled that leap year or not, the months will
always be equal to 12 months.

decision or the unacted claim with the Court of Tax Appeals.

In this case, Aichi did not wait for the decision of the CIR or the

simultaneously.
Aichis assertion that the non-observance of this rule is not fatal has
no legal basis. What Section 112 refers to when it says that the filing
may be made within 2 years after the close of the taxable quarter
when the sales were made, is the period to apply for the issuance of
the tax credit certificate/refund WITH THE CIR, and not appeals
made to the CTA.

WESTERN MINDANAO v. CIR (Austria)

MONTERO // 3A TAX DIGESTS

[GR. No. 181136; June 13, 2012]

Corporation (WMPC) did not contain the phrase "zero-rated," as required

under Revenue Regulations No. 7 95 (RR 795).

If you liked it, then you shoulda put a [stamp] on it oh oh oh

Petitioner WMPC is a domestic corporation engaged in the

production and sale of electricity [to the NPC].

Recit-Ready:
Facts: This case is about the denial of the CTA En Banc of the Petition

Petitioner alleges that it sells electricity solely to the National

for refund of unutilized input Value Added Tax (VAT) of petitioner

Power Corporation (NPC), which is in turn exempt from the

Western Mindanao Power Corporation (WMPC), a seller of

payment of all forms of taxes, duties, fees and imposts,

electricity to NAPOCOR (exempted entity), on the ground that the

pursuant to Section 132 of Republic Act (R.A.) No. 6395 (An Act

Official Receipts of petitioner did not contain the phrase "zero--

Revising the Charter of the National Power Corporation).

rated," as required under Revenue Regulations No. 7-95 (RR 7--

In view thereof and pursuant to Section 108(B) (3) of the

National Internal Revenue Code (NIRC), petitioner's power

95).

generation services to NPC is zero-rated.

Issue: Whether the CTA En Banc seriously erred in dismissing the claim

Under Section 112(A) of the NIRC, 4 a VAT-registered taxpayer may,

of petitioner for a refund or tax credit on input tax on the ground

within two years after the close of the taxable quarter, apply for the

that the latter's Official Receipts do not contain the phrase zero--

issuance of a tax credit or refund of creditable input tax due or paid and

rated.

attributable to zero-rated or effectively zero-rated sales.

Held:

Hence, on 20 June 2000 and 13 June 2001, WMPC filed with

NO. The CTA En Banc did not err in dismissing the claim for

the Commissioner of Internal Revenue (CIR) applications for a

tax credit for failing to meet the documentary and evidentiary

tax credit certificate of its input VAT covering the taxable 3rd

requirements. The Supreme Court has consistently held as

and 4th quarters of 1999 (amounting to P3,675,026.67) and all

fatal the failure to print the word "zero-rated" on the Value-

the taxable quarters of 2000 (amounting to P5,649,256.81)

Added Tax (VAT) invoices or official receipts in claims for a

refund or credit of input VAT on zero-rated sales.

CTA Division: Noting that the CIR was not acting on its application, AND
fearing that its claim would soon be barred by prescription, WMPC on 28
September 2001 filed with the Court of Tax Appeals (CTA) in Division a

Facts:

This is a petition for review of CTA En Bancs Resolution denying the

Petition for refund of unutilized input Value Added Tax (VAT) on the
ground that the Official Receipts of petitioner Western Mindanao Power

Petition for Review docketed as C.T.A. Case No. 6335, seeking

refund/tax credit certificates for the total amount of P9,324,283.30.
o

CIR Comment: WMPC was not entitled to the latter's claim for a
tax refund in view of its failure to comply with the invoicing
requirements under Section 113 of the NIRC in relation to

MONTERO // 3A TAX DIGESTS

Section 4.1081 of RR 795 (see no.5 the word zero rated

imprinted on the invoice covering zero rated sales.
o

prominently" on the VAT invoice or official

receipt for sales subject to zero percent (0%)

WMPC: countered that

VATappeared in Section 113 of the NIRC

the invoicing and accounting requirements laid down in

only after it was amended by Section 11 of

RR 795 were merely "compliance requirements," which

R.A. 9337.8

were not indispensable to establish the claim for refund

of excess and unutilized input VAT.

considering that it took effect only on 1 July 2005, or

Also, Section 113 of the NIRC prevailing at the time the

long after petitioner filed its claim for a tax refund, and

sales transactions were made did not expressly state

considering further that the RR 795 is punitive in

that failure to comply with all the invoicing requirements

nature.

would result in the disallowance of a tax credit refund.

This amendment cannot be applied retroactively

Further, since there was no statutory requirement for

The express requirementthat "the term 'zero

imprinting the phrase "zero-rated" on official receipts

rated

prior to 1 July 2005, the RR 795 constituted undue

sale'

shall

written

printed

expansion of the scope of the legislation it sought to

SECTION 4.1081. Invoicing [Link] VAT registered persons shall, for every

implement.

sale or lease of goods or properties or services, issue duly registered receipts or sales or
commercial invoices which must show: 1. the name, TIN and address of seller; 2. date of

Petitioner moved for reconsideration, but the motion was denied

transaction; 3. quantity, unit cost and description of merchandise or nature of service; 4. the

CTA Second Division Decision: On 1 September 2006, the CTA Second

name, TIN, business style, if any, and address of the VAT registered purchaser, customer or

Division dismissed the Petition. It held that:

client; 5. the word "zero rated" imprinted on the invoice covering zero rated sales; and

6. the invoice value or consideration. In the case of sale of real property subject to VAT and

while petitioner submitted in evidence its Quarterly VAT Returns

for the periods applied for, "the same do not reflect any zero--

where the zonal or market value is higher than the actual consideration, the VAT shall be
separately indicated in the invoice or receipt.

rated or effectively zero-rated sales allegedly incurred during

Only VAT-registered persons are required to print their TIN followed by the word

said periods. The spaces provided for such amounts were left

"VAT" in their invoice or receipts and this shall be considered as a "VAT Invoice." All

blank, which only shows that there existed no zero rated or

purchases covered by invoices other than "VAT" Invoice" shall not give rise to any

effectively zero-rated sales for the 3rd and 4th quarters of 1999

input tax.

and the four quarters of 2000."

If the taxable person is also engaged in exempt operations, he should issue separate

invoices or receipts for the taxable and exempt operations. A "VAT Invoice" shall be issued

Moreover, it found that petitioner's VAT Invoices and Official

only for sales of goods, properties or services subject to VAT imposed in Sections 100 and

Receipts did not contain on their face the phrase "zero-rated,"

102 of the Code. The invoice or receipt shall be prepared at least in duplicate, the original to

contrary to Section 4.1081 of RR 795.

be given to the buyer and the duplicate to be retained by the seller as part of his accounting
records." (Underscoring supplied.)

CTA En Banc Decision: dismissing the appeal and affirming the CTA
ruling.

MONTERO // 3A TAX DIGESTS

In addition, the CTA En Banc noted that petitioner's Official

Refunds or Tax Credits of Input Tax. (A) Zerorated or Effectively Zero-

Receipts and VAT Invoices did not have the word "zero-rated"
imprinted/stamped thereon, contrary to the clear mandate of

invoice or official receipt, which may only be considered as such when it

Section 4.1081 of RR 795.

rated Sales.)
Under the NIRC, a creditable input tax should be evidenced by a VAT
complies with the requirements of RR 795, particularly Section 4.1081.
o This section requires, among others, that "(i)f the sale

Dissenting of Justice Ernesto Acosta; the absence of the term

"zero-rated" in an invoice or official receipt does not affect its

is subject to zero percent (0%) value-added tax, the

admissibility or competency as evidence in support of a refund

term 'zero-rated sale' shall be written or printed

claim. Also, assuming that stamping the term "zero-rated" on an

invoice or official receipt is a requirement of the current NIRC,
the denial of a refund claim is not the imposable penalty for
failure to comply with that requirement.

WMPC filed a Motion for Reconsideration, which was denied by the CTA
En Banc

Issue/s: Whether the CTA En Banc seriously erred in dismissing the claim of
petitioner for a refund or tax credit on input tax on the ground that the latter's

prominently on the invoice or receipt.

We are not persuaded by petitioner's argument that RR 7-95 constitutes
undue expansion of the scope of the legislation it seeks to implement on
the ground that the statutory requirement for imprinting the phrase "zero
rated" on VAT official receipts appears only in Republic Act No. 9337.
This law took effect on 1 July 2005, or long after petitioner had filed its
claim for a refund.
o RR 795, which took effect on 1 January 1996, proceeds
from the rulemaking authority granted to the Secretary of

Official Receipts do not contain the phrase zero-rated NO, receipts should

Finance by the NIRC for the efficient enforcement of the

contain zero-rated
Held/Ratio: Petition DENIED.

Philippines v. Commissioner of Internal Revenue: The

provision is "reasonable and is in accord with the efficient

NO. The CTA En Banc did not err in dismissing the claim for tax credit

collection of VAT from the covered sales of goods and

for failing to meet the documentary and evidentiary requirements. The

Supreme Court has consistently held as fatal the failure to print the
word "zero-rated" on the Value-Added Tax (VAT) invoices or official
receipts in claims for a refund or credit of input VAT on zero-rated sales

In the present case, petitioner's claim for a refund or tax credit of input
VAT is anchored on Section 112(A) of the NIRC (see codal: Section 112.

same Tax Code and its amendments

In Panasonic Communications Imaging Corporation of the

services.
In Kepco Philippines Revenue Corporation v. Commissioner
of Internal: the subsequent incorporation of Section 4.1081
of RR 795 in Section 113 (B) (2) (c) of R.A. 9337 actually
confirmed the validity of the imprinting requirement on VAT
invoices or official receiptsa case falling under the
principle

legislative

approval

administrative

interpretation by reenactment this Court has consistently

MONTERO // 3A TAX DIGESTS

held as fatal the failure to print the word "zero-rated" on the

Being a derogation of the sovereign authority, a statute granting tax

VAT invoices or official receipts in claims for a refund or

exemption is strictly construed against the person or entity claiming

credit of input VAT on zero-rated sales, even if the claims

the exemption.
o When based on such statute, a claim for tax refund

were made prior to the effectivity of R.A. 9337.20

In addition, it is notable that the CTA Second Division and the CTA En
Banc, including Presiding Justice Acosta in his Concurring and

taxpayer-claimant applies to the claim.

Dissenting Opinion, both found that petitioner failed to sufficiently

substantiate the existence of its effectively zero-rated sales to NPC

for the 3rd and 4th quarters of taxable year 1999, as well as all four

COMMISSIONER OF INTERNAL REVENUE v. SAN ROQUE

quarters of taxable year 2000

It must also be noted that the CTA is a highly specialized court

(BAADERA)

dedicated exclusively to the study and consideration of revenue--

The 120+30 day rule//two-year judicial claim rule//operative fact rule case

not be disturbed on appeal.

A taxpayer engaged in zero-rated or effectively zero rated sale may
apply for the issuance of a tax credit certificate, or refund of

partakes of the nature of an exemption.

Hence, the same rule of strict interpretation against the

creditable input tax due or paid, attributable to the sale

Requirements: In a claim for tax refund or tax credit, the applicant must
prove not only entitlement to the grant of the claim under substantive
law. It must also show satisfaction of all the documentary and
evidentiary requirements for an administrative claim for a refund or
tax credit.
o Hence, the mere fact that petitioner's application for zero-rating has
been approved by the CIR does not, by itself, justify the grant of a
o

refund or tax credit.

The taxpayer claiming the refund must further comply with the
invoicing and accounting requirements mandated by the NIRC, as
well as by revenue regulations implementing them.

[GR. No. 187485; February 12, 2013]

Recit-Ready:
Facts: This case consists of three cases filed by San Roque, Taganito,
and Philex for their tax refund. San Roques claim was granted by
the court citing Atlas and RMC 49-03 wherein both claimed that a
taxpayer may file a judicial claim before the lapse of the 120 days.
Thus, the judicial claim of San Roque is valid despite it being filed
13 days after the administrative claim was filed. In Taganito, the
court denied the refund since Taganito filed the judicial claim just
92 days after its administrative claim. The court cited Mirant and
Aichi claiming the periods are mandatory. One Justice dissented
to the decision claiming the contrary. Philex on the other hand
only filed the case for a judicial claim after CIRs inaction for two
years on their administrative claim. The court denied the refund
since the claim was filed beyond the two-year prescription period
and that Philex should have filed their claim after the lapse of 120
days. The court stated in the DIVISION level that judicial claims
should be filed within the two-year prescription. At the En Banc

MONTERO // 3A TAX DIGESTS

level, the court similarly affirmed the denial but added that the law

7) WON existing jurisprudence does not distinguish as to the filing dates

gives the taxpayer only 30 days after the lapse of 120 days to file

of administrative and judicial claims as long as they are made within

their claim. Philex filed their claim 426 days after the lapse of 30

the two-year period.

NO
8) WON Section 4.106-2(c) of Revenue Regulations No. 7-95 allows

days so denied.

Issue/s:
1) WON a taxpayer could file a judicial claim without having to wait the
decision on their administrative claim. In short, can the taxpayer file a
judicial claim without waiting for the lapse of 120 days? Also, does the
Atlas doctrine still apply?
NO with the exception of Philex and as for Atlas, it is not applicable
2) WON the 30-day period for judicial appeal falls within the two-year
period for prescription of the refund.
NO
3) WON the word excess mentioned under Section 229 is similar to
excess under 110(B) and 112(A) for purposes of counting the
reckoning period and the prescription period of refund.
NO
4) WON the Atlas doctrine allows the filing of judicial claims despite the

premature filing of judicial claims.

NO
Held:
1) NO with exception with Philex. San Roque must wait for the 120 days
as the requirement is mandated by law and that no decision can
result without the lapse of 120 days therefore CTA cannot also acquire
jurisdiction. For Philex, the court allowed to file ahead of 120 days
citing BIR Ruling No. DA-489-03. Philex was really late in filing.
2) NO. Careful scrutiny of the Code reveals that the two-year period only
refers to administrative claims and not judicial claims.
3) NO. Section 229s term "excessively collected occurs when the
person liable for the tax actually pays more than what is legally due.

lapse of 120 days and whether Section 112(C)s use of may allows

The prescriptive period is reckoned from the date the person liable for

the filing of judicial claim before the 120 day lapse.

NO
5) WON Revenue Memorandum Circular No. 49-03 (RMC 49-03) allows

the tax pays the tax. Alternatively, under Section 110(B) and Section
112(A), the prescriptive period for filing a judicial claim for "excess"

the filing of claims before the lapse of 120 days.

NO
6) WON BIR Ruling No. DA-489-03 is an exception to the mandatory 120

when the sale was made by the person legally liable to pay the

day rule.
YES but only from 10 December 2003 up to its reversal by this Court
in Aichi on 6 October 2010. (Take note: Operative Fact question
according to reviewers)

input VAT is two years from the close of the TAXABLE QUARTER,
output VAT. Aside from the reckoning date, it is important also to know
this since under Section 229, tax can be claimed as a credit or refund
while Sections 110(B) and Section 112(A) require first that the
taxpayer must have an output VAT to which input tax would be
attributed to (with the exception of course of zero-rated transactions)

MONTERO // 3A TAX DIGESTS

with the Government of the Philippines or any of its subdivision,

4) NO. Atlas doctrine has nothing to do with 120+30 days and whatever
its doctrine was, it was abandoned last June 2007 with the
pronouncement in Mirant. May refers to the choice of the taxpayer on

National Power Corporation ("NPC") to develop hydro-potential of the

whether they would like to file an appeal or not

Lower Agno River and generate additional power and energy for the

5) NO. The RMC 49-03 clarifies that the filing of judicial claims does not
divest the CIR of his jurisdiction to decide on administrative claims

Roque allegedly incurred, excess input VAT in the amount of

in Aichi on 6 October 2010. BIR Ruling No. DA-489-03 is a general

559,709,337.54 for taxable year 2001. On March 28, 2003 it then filed

interpretative rule and the Commissioner cannot then question the

with BIR for a refund.

o CIRs inaction though prompted San Roque to file a Petition

CTAs jurisdiction and equitable estoppel has set in.

that compliance with the 120-day mandatory period is inconsequential

Luzon Power Grid, by building the San Roque Multi-Purpose Project.

On the construction and development of the San Roque Multi- Purpose
Project which comprises of the dam, spillway and power plant, San

6) YES from 10 December 2003 up to its reversal by this Court

7) NO. None of these five cases mention, cite, discuss, rule or even hint

instrumentality or agency.
San Roque entered into a Power Purchase Agreement ("PPA") with the

for Review with CTA on April 10, 2003. (13 days)

CTA denied the petition for lack of recorded zero-rated or effectively zerorated sales; failure to submit documents specifically identifying the

as long as the administrative and judicial claims are filed within the

purchased goods/services related to the claimed input VAT.

o CTA required San Roque to prove the existence of Sec. 112

two-year prescriptive period.

(B) of RA 8424 namely:

(1) it is a VAT-registered entity;
(2) its input taxes claimed were paid on capital

8) NO. Section 4.106-2(c) of Revenue Regulations No. 7-95 did not allow
premature filing of judicial claims. Even assuming the contrary, Section
4.106-2(c), a mere administrative issuance, becomes inconsistent with

goods duly supported by VAT invoices and/or

Section 112(D), a later law. Obviously, the later law prevails over a
prior inconsistent administrative issuance

payments on capital goods against any output VAT

Facts:
G.R. No. 187485

CIR v. San Roque Power Corporation (San Roque)

official receipts;
(3) it did not offset or apply the claimed input VAT
liability; and
(4) its claim for refund was filed within the two-year

prescriptive period
CTA Second Division reversed the decision and found that San Roque

San Roque is a domestic corporation whose function is to design,

construct, erect, assemble, own, commission and operate power-

complied with the first, third, and fourth requirements.

San Roque filed a Motion for New Trial and/or Reconsideration

generating plants and related facilities pursuant to and under contract

MONTERO // 3A TAX DIGESTS

CTA Second Division found legal basis to partially grant San Roques

provision. The respondent is also covered by the two (2)

claim. The CTA Second Division ordered the Commissioner to REFUND

or issue a tax credit in favor of San Roque in the amount of

year prescriptive period.

In the case of Atlas Consolidated Mining and Development

483,797,599.65
o The amount represents San Roques unutilized input VAT

Corporation vs. Commissioner of Internal Revenue (Atlas)

on its purchases of capital goods and services for the

tax is reckoned from the date of the filing of the

taxable year 2001. (Compared to the 1

decision, court

quarterly VAT return and payment of the tax due. If the

managed to amend their decision since they hired now an

said period is about to expire but the BIR has not yet

independent CPA to do the computation WOW!)

The court reasoned that the deduction from the total

acted on the application for refund, the taxpayer may

amount asked by San Roque was based on the discrepancy

of evidence it presented. The receipts and invoices

two year period.

In Gibbs, the court held that if the two-year period

contradicted the amount that is reflected in its books.

is about to expire but no reply yet has been given

Further
Also, San Roques claim for refund or tax credit of its

by BIR, the taxpayer may start the petition to Court

unutilized input VAT for the last quarter of 2001 was denied

period without awaiting the decision of the

the two-year prescriptive period for filing a claim for input

interpose a petition for review with this Court within the

of Tax Appeals before the end of the two-year

as well since there is no record of sales that would relate to

zero-rated or effectively zero-rated transaction.

CIR appealed but was still denied by CTA En Banc reasoning:
o It is true that Section 112(D) 3 of the abovementioned

not bound to wait indefinitely for no reason for

whatever action respondent (herein petitioner) may

provision applies to the present case. However, what the

petitioner failed to consider is Section 112(A) 4 of the same
3

SECTION 112(D) Period within which Refund or Tax Credit of Input Taxes shall be
Made. - In proper cases, the Commissioner shall grant a refund or issue the tax credit
certificate for creditable input taxes within one hundred twenty (120) days from the date
of submission of complete documents in support of the application filed in accordance
with Subsections (A) and (B) hereof.
4

SECTION 112 (A) Zero-rated or Effectively Zero-rated Sales. - Any VAT-registered

person, whose sales are zero-rated or effectively zero-rated may, within two (2) years
after the close of the taxable quarter when the sales were made, apply for the issuance
of a tax credit certificate or refund of creditable input tax due or paid attributable to such
sales, except transitional input tax, to the extent that such input tax has not been applied

Collector.
This Court ruled in several cases that the Court is

take.
Also, A-17 of Revenue Memorandum Circular No.
42-2003 states: In cases where the taxpayer has
filed a "Petition for Review" with the Court of

against output tax: Provided, however, That in the case of zero-rated sales under Section
106(A)(2)(a)(1),(2) and (B) and Section 108 (B)(1) and (2), the acceptable foreign currency
exchange proceeds thereof had been duly accounted for in accordance with the rules and
regulations of the Bangko Sentral ng Pilipinas (BSP): Provided, further, That where the
taxpayer is engaged in zero-rated or effectively zero-rated sale and also in taxable or
exempt sale of goods or properties or services, and the amount of creditable input tax due
or paid cannot be directly and entirely attributed to any one of the transactions, it shall be
allocated proportionately on the basis of the volume of sales.

MONTERO // 3A TAX DIGESTS

Tax Appeals involving a claim for refund/TCC

Taganito filed all its Monthly VAT Declarations and Quarterly Vat Returns

that is pending at the administrative agency

for the period January 1, 2005. Taganito reported zero-rated sales

(Bureau of Internal Revenue or OSS-DOF), the

amounting to P1,446,854,034.68; input VAT on its domestic purchases

administrative agency and the tax court may

and importations of goods (other than capital goods) and services

act on the case separately.

amounting to P2,314,730.43; and input VAT on its domestic purchases

and importations of capital goods amounting to P6,050,933.95. This

Lastly, it is apparent from the following provisions of Revenue

amounted to P8,365,664.38
o November 14, 2006, Taganito filed for a tax credit/refund of

Memorandum Circular No. 49-03 dated August 18, 2003, that [the CIR]
knows that claims for VAT refund or tax credit filed with the Court [of Tax
Appeals] can proceed simultaneously with the ones filed with the BIR and

VAT is about to lapse without action on the part of the CIR, Taganito filed

that taxpayers need not wait for the lapse of the subject 120-day period
(This pronouncement is important for the fifth issue)

G.R. No. 196113

Taganito Mining Corporation v. CIR (Taganito)
Taganito Mining Corporation, is a corporation whose business is to carry
on the business, for itself and for others, of mining lode and/or placer
mining,

developing,

converting,

smelting,

exploiting,
treating,

extracting,
refining,

milling,
preparing

concentrating,
for

market,

manufacturing, buying, selling, exchanging, shipping, transporting, and

otherwise producing and dealing in nickel, chromite, cobalt, gold, silver,
copper, lead, zinc, brass, iron, steel, limestone, and all kinds of ores,
metals and their by-products and which by-products thereof of every kind
and description and by whatsoever process the same can be or may
hereafter be produced and generally and without limit as to amount, to
buy, sell, locate, exchange, lease, acquire and deal in lands, mines, and
mineral rights and claims and to conduct all business appertaining thereto
o (In short, they buy, sell, and/or produce ores or business
related thereto)

its supposed input VAT amounting to 8,365,664.38

As the statutory period within which to file a claim for refund for said input
the instant Petition for Review on February 17, 2007.(less than 3 months)
Taganito sent a letter January 1, 2005 to December 31, 2005.
On March 2007, CIR replied and ruled:
o The court has no jurisdiction over the entertain the instant
petition for review for failure on the part of Taganito to
comply with the provision of Section 112 (D) of the 1997
Tax Code which provides
(D) Period within which refund or Tax Credit of
Input Taxes shall be Made. In proper cases, the
Commissioner shall grant a refund or issue the tax
credit certificate for creditable input taxes within
one hundred (120) days from the date of
submission of complete documents in support
of the application filed in accordance with
Subsections (A) and (B) hereof.
In cases of full or partial denial for tax refund or tax
credit,

the

failure

the

part

the

Commissioner to act on the application within the

period prescribed above, the taxpayer affected

MONTERO // 3A TAX DIGESTS

may, within thirty (30) days from the receipt of

Company of Asia, Inc. (Aichi) and Commisioner of Internal

the decision denying the claim or after the

Revenue v. Mirant Pagbilao Corporation (Mirant).

The cases ruled that the two-year prescriptive

expiration

the

one

hundred

twenty

dayperiod, appeal the decision or the unacted

period to file a refund for input VAT arising from

claim with the Court of Tax Appeals.

CIR claimed that the 120 days has already passed.

close of the taxable quarter when the sales

zero-rated sales should be reckoned from the

Taganito filed the administrative claim on November 14,

2006 and subsequently the petition for review, herein

await the decision of the Commissioner or the

petition, was filed last February 14, 2007.

CTA ruled that Taganito complied with the requirements of Section 112(A)

lapse of 120-day period prescribed in Section

of RA 8424, as amended, to be entitled to a tax refund or credit of input

VAT attributable to zero-rated or effectively zero-rated sales.
o Records show that Taganitos administrative claim filed on

November 14, 2006, which was amended on November 29,

filed. Taganito filed its Petition for Review before the CTA

2006, and the Petition for Review filed with this Court on

Second Division on 14 February 2007. The judicial claim

February 14, 2007 are well within the two-year prescriptive

was filed after the lapse of only 92 days from the filing of its

period, reckoned from March 31, 2005, June 30, 2005,

administrative claim before the CIR, in violation of the 120-

September 30, 2005, and December 31, 2005, respectively,

day period prescribed in Section 112(D) of the 1997 Tax

January 1, 2005 to December 31, 2005.

Commissioner filed a Reconsideration.
CTA En Banc reversed the decision and denied the refund to Taganito
claiming:
o

The CTA EB declared that Section 112(A) and (B) of the

1997 Tax Code both set forth the reckoning of the two-year
prescriptive period for filing a claim for tax refund or credit
over input VAT to be the close of the taxable quarter when

112(D) amounts to a premature filing.

Although the administrative claim was filed on time, the CTA
EB found that Taganitos judicial claim was prematurely

the close of each taxable quarter covering the period

were made.
Aichi further emphasized that the failure to

the sales were made.

The CTA EB also relied on this Courts rulings in the cases
of Commissioner of Internal Revenue v. Aichi Forging

Code.
Associate Justice Bautista dissented to the decision claiming that the

taxpayer has a right to file before the lapse of 120 days.

CTA En Banc denied the MR.

G.R. No. 197156

Philex Mining Corporation v. CIR (Philex)

Philex is a corporation engaged in the mining business, which includes

the exploration and operation of mine properties and commercial

production and marketing of mine products

Philex filed its Original VAT Return for the third quarter of taxable year
2005 and Amended VAT Return for the same quarter on December 1,
2005.

MONTERO // 3A TAX DIGESTS

On March 20, 2006, Philex filed its claim for refund/tax

a judicial claim without waiting for the lapse of 120 days? Also, does

credit of the amount of 23,956,732.44

Due to CIRs failure to act on such claim, on October 17, 2007, pursuant

the Atlas doctrine still apply?

NO with the exception of Philex and as for Atlas, it is not applicable
2) WON the 30-day period for judicial appeal falls within the two-year

to Sections 112 and 229 of the NIRC of 1997, as amended, Philex filed a

Petition for Review.

CTA Division ruled:
o Philexs claim prescribed. The CTA Second Division ruled
that the two-year prescriptive period specified in Section
112(A) of RA 8424, as amended, applies not only to the
filing of the administrative claim with the BIR, but also
to the filing of the judicial claim with the CTA. (So
o

petition for review should be within the two-years)

Since Philexs claim covered the 3rd quarter of 2005, its
administrative claim filed on 20 March 2006 was timely filed,
while its judicial claim filed on 17 October 2007 was filed

late.
MR was denied
CTA En Banc AFFIRMED:
o Records show that an administrative claim was filed on
March 20, 2006. The CIR has 120 days, or until July 18,
2006, within which to decide the claim. Within 30 days
from the lapse of the 120-day period, or from July 19,
2006 until August 17, 2006, Philex should have elevated
its claim for refund to the CTA. However in this case,
Philex filed its Petition for Review only on October 17, 2007,
which is 426 days way beyond the 30- day period
prescribed by law.

Issues:
1) WON a taxpayer could file a judicial claim without having to wait the
decision on their administrative claim. In short, can the taxpayer file

period for prescription of the refund.

NO
3) WON the word excess mentioned under Section 229 is similar to
excess under 110(B) and 112(A) for purposes of counting the
reckoning period and the prescription period of refund.
NO
4) WON the Atlas doctrine allows the filing of judicial claims despite
the lapse of 120 days and whether Section 112(C)s use of may
allows the filing of judicial claim before the 120 day lapse.
NO
5) WON Revenue Memorandum Circular No. 49-03 (RMC 49-03) allows
the filing of claims before the lapse of 120 days.
NO
6) WON BIR Ruling No. DA-489-03 is an exception to the mandatory 120
day rule.
YES but only from 10 December 2003 up to its reversal by this Court
in Aichi on 6 October 2010. (Take note: Operative Fact question
according to reviewers)
7) WON existing jurisprudence does not distinguish as to the filing
dates of administrative and judicial claims as long as they are made
within the two-year period.
NO
8) WON Section 4.106-2(c) of Revenue Regulations No. 7-95 allows
premature filing of judicial claims.
NO
Held/Ratio: WHEREFORE, the Court hereby (1) GRANTS the petition of the
Commissioner of Internal Revenue in G.R. No. 187485 to DENY the

MONTERO // 3A TAX DIGESTS

cause of action, with the effect that the CTA does not

P483,797,599.65 tax refund or credit claim of San Roque Power Corporation;

(2) GRANTS the petition of Taganito Mining Corporation in G.R. No. 196113
for a tax refund or credit of P8,365,664.38; and (3)DENIES the petition of

acquire jurisdiction over the taxpayers petition.

CTA expressly provides that its jurisdiction is to review

Philex Mining Corporation in G.R. No. 197156 for a tax refund or credit of

on appeal "decisions for refunds of taxes. Without

P23,956,732.44..

waiting for the period, there can be no decision that

could be reviewed by CTA. The charter of the CTA also

NO with exception with Philex. San Roque must wait for the 120

expressly provides that if the Commissioner fails to

days as the requirement is mandated by law and that no decision

decide within "a specific period" required by law, such

can result without the lapse of 120 days therefore CTA cannot also
acquire jurisdiction. For Philex, the court allowed to file ahead of
120 days citing BIR Ruling No. DA-489-03. Philex was really late in
filing.

"inaction shall be deemed a denial"

San Roque cannot also claim being misled, misguided or confused by
the Atlas doctrine because San Roque filed its petition for review
with

the

than

four

years

before Atlas was

date of payment of the output VAT, not from the close of

day period to lapse before filing its judicial claim. Also, San Roque

two-year prescriptive period should be counted from the

Base from records, San Roque did not wait for first wait for the 120filed

CTA

promulgated.
O
In any event, the Atlas doctrine merely stated that the

SAN ROQUE
O

its

judicial

claim

than

four

the taxable quarter.

In Atlas the petitioner there filed their tax return

(4)

years BEFORE the Atlas doctrine was promulgated.

Clearly, San Roque failed to comply with the 120-day waiting period,

after the close of quarter (e.g. Quarter closed

on 30 June 1990, Atlas only paid on 20 July

the time expressly given by law to the Commissioner to decide

whether to grant or deny San Roques application for tax refund or

credit. It is indisputable that compliance with the 120-day waiting

period ends on 20 July 1992 or two years after

period is mandatory and jurisdictional.

O
This waiting period has been in our statute books

1990)
The court ruled that the two-year prescriptive

for more than fifteen (15) years before San Roque

the filing of return.

The Atlas doctrine does not interpret, expressly or

filed its judicial claim. In the past, it was only 60 days.

Failure to comply with the 120-day waiting period

impliedly, the 120+30 day periods.

Atlas doctrine cannot be invoked by anyone to
disregard compliance with the 30-day mandatory

violates a mandatory provision of law. It violates the

doctrine of exhaustion of administrative remedies
and renders the petition premature and thus without a

and jurisdictional period.

Atlas is immaterial

MONTERO // 3A TAX DIGESTS

At the time San Roque filed its petition for review with the CTA,

lapse of the 120-day period. In any event, whether governed by

the 120+30 day mandatory periods were already in the law.

jurisprudence before, during, or after the Atlas case, Philexs

Section 112(C) expressly grants the Commissioner 120 days

within which to decide the taxpayers claim.

judicial claim will have to be rejected because of late filing.

The Atlas doctrine cannot save Philex (so immaterial) from the late
filing of its judicial claim. The inaction of the Commissioner on
Philexs claim during the 120-day period is, by express provision of

TAGANITO
O

Like San Roque, Taganito also filed its petition for review with the CTA
without waiting for the 120-day period to lapse. Also, like San Roque,
Taganito

filed

its

judicial

claim four

months

(4)

before the

promulgation of the Atlas doctrine.

HOWEVER UNLIKE SAN ROQUE it invoked BIR Ruling No. DA-489-

035 but before the adoption of the Aichi doctrine (explained later).
Thus Taganitos refund is valid.

PHILEX
O

To recall, the Commissioner had until 17 July 2006, the last day of the
120-day period, to decide Philexs claim. Since the Commissioner did
not act on Philexs claim on or before 17 July 2006, Philex had until 17
August 2006, the last day of the 30-day period, to file its judicial
claim. The CTA EB held that 17 August 2006 was indeed the last

day for Philex to file its judicial claim.

However, Philex filed its Petition for Review with the CTA only on 17

law, "deemed a denial" of Philexs claim.

2) NO. Careful scrutiny of the Code reveals that the two-year period
only refers to administrative claims and not judicial claims.
o First, Section 112(A) clearly, plainly, and unequivocally provides that
the taxpayer "may, within two (2) years after the close of the taxable
quarter when the sales were made, apply for the issuance of a tax
credit certificate or refund of the creditable input tax due or paid to
such sales.
o

within two years whether it would be on the last or first.

o Second, Section 112(C) provides that the Commissioner shall decide
the application for refund or credit "within one hundred twenty (120)
days from the date of submission of complete documents in support
of the application filed in accordance with Subsection (A)."
o The highlighted part above means that the provision
ONLY REFERS TO ADMINISTRATIVE CLAIMS.
In Aichi, the words clearly refer to refund or

October 2007, or four hundred twenty-six (426) days after the last day
of filing. In short, Philex was late by one year and 61 days in filing
O

its judicial claim.

Compared to the previous two cases, Philex filed its judicial claim long
after the expiration of the 120-day period, in fact 426 days after the

BIR RULING NO. DA-489-03 - Taxpayer-claimant need not wait for the lapse of the
120-day period before it could seek judicial relief with the CTA by way of Petition for
Review.

"Within two (2) years," which means at anytime

credit not appeal to CTA.

Stated otherwise, the two-year prescriptive period
does not refer to the filing of the judicial claim with
the CTA but to the filing of the administrative claim

with the Commissioner.

o Third, if the 30-day period, or any part of it, is required to fall within the
two-year prescriptive period (equivalent to 730 days), then the

MONTERO // 3A TAX DIGESTS

taxpayer must file his administrative claim for refund or credit within

o The input VAT is not "excessively" collected as understood under

the first 610 days of the two-year prescriptive period.

o The theory that the 30-day period must fall within the two-year

Section 2296 because at the time the input VAT is collected the
amount paid is correct and proper.
o To recall, an input VAT is a tax liability of, and legally

prescriptive period adds a condition that is not found in the law.

o The taxpayer can file his administrative claim for refund or credit

paid by, a VAT-registered seller. The second VAT-

at anytime within the two-year prescriptive period.

registered person, who is not legally liable for the input

VAT, is the one who applies the input VAT as credit for

3) NO. Section 229s term "excessively collected occurs when the

his own output VAT. If the input VAT is in fact

person liable for the tax actually pays more than what is legally due.

"excessively" collected as understood under Section

The prescriptive period is reckoned from the date the person liable

229, then it is the first VAT-registered person - the

for the tax pays the tax. Alternatively, under Section 110(B) and

taxpayer who is legally liable and who is deemed to have

Section 112(A), the prescriptive period for filing a judicial claim for
"excess" input VAT is two years from the close of the TAXABLE

legally paid for the input VAT.

o The person legally liable for the input VAT cannot claim that he

QUARTER, when the sale was made by the person legally liable to

overpaid the input VAT by the mere existence of an "excess" input

pay the output VAT. Aside from the reckoning date, it is important

VAT. The term "excess" input VAT simply means that the input

also to know this since under Section 229, tax can be claimed as a

VAT available as credit exceeds the output VAT, not that the input

credit or refund while Sections 110(B) and Section 112(A) require

VAT is excessively collected because it is more than what is

first that the taxpayer must have an output VAT to which input tax

legally due.

would be attributed to (with the exception of course of zero-rated

transactions).

SECTION 229. Recovery of Tax Erroneously or Illegally Collected. - No suit or

proceeding shall be maintained in any court for the recovery of any national internal
revenue tax hereafter alleged to have been erroneously or illegally assessed or collected, or
of any penalty claimed to have been collected without authority, or of any sum alleged to
have been excessively or in any manner wrongfully collected, until a claim for refund or
credit has been duly filed with the Commissioner; but such suit or proceeding may be
maintained, whether or not such tax, penalty, or sum has been paid under protest or
duress.
In any case, no such suit or proceeding shall be filed after the expiration of two (2)
years from the date of payment of the tax or penalty regardless of any supervening cause
that may arise after payment: Provided, however, That the Commissioner may, even without
a written claim therefor, refund or credit any tax, where on the face of the return upon which
payment was made, such payment appears clearly to have been erroneously paid.

MONTERO // 3A TAX DIGESTS

o Under Section 229, the prescriptive period for filing a judicial claim for

Thus, a non zero-rated VAT-registered taxpayer who has

refund is two years.

o The prescriptive period is reckoned from the date the

no output VAT because he has no sales cannot claim a

person liable for the tax pays the tax.

This means the date when the taxpayer pays

VAT System. (Exception is if you are zero-rated)

o The said unused input VAT is then NOT excess.
o The VAT System does not allow such refund or credit.

than

should

have

under

the

assessment.
Taxpayer here is the person legally

tax refund or credit of his unused input VAT under the

Such "excess" input VAT is not an "excessively"

liable to pay the tax and NOT the

collected tax under Section 229.

o As the Court held in Mirant, Section 229 should "apply only to

person to whom the tax is passed

instances of erroneous payment or illegal collection of internal

on as part of the purchase price.

o Under Section 110(B) and Section 112(A), the prescriptive period for

revenue taxes." Erroneous or wrongful payment includes excessive

filing a judicial claim for "excess" input VAT is two years from the close
of the taxable quarter when the sale was made by the person legally

due.
o Any suggestion that the "excess" input VAT under the VAT System is

liable to pay the output VAT. This prescriptive period has no relation to

an "excessively" collected tax under Section 229 may lead taxpayers

the date of payment of the "excess" input VAT. The "excess" input VAT

to file a claim for refund or credit for such "excess" input VAT under

may have been paid for more than two years but this does not bar the

Section 229 as an ordinary tax refund or credit outside of the VAT

filing of a judicial claim for "excess" VAT under Section 112(A), which

System.

has a different reckoning period from Section 229.

o The person claiming the refund or credit of the input VAT
is not the person who legally paid the input VAT.
o To recall, under Section 110(B), a taxpayer can apply his input VAT
only against his output VAT. The only exception is when the taxpayer
is expressly "zero-rated or effectively zero-rated" under the law, like
companies generating power through renewable sources of energy.

payment because they all refer to payment of taxes not legally

Under Section 229, mere payment of a tax beyond what

is legally due can be claimed as a refund or credit.
There is no requirement under Section 229 for an output
VAT or subsequent sale of goods, properties, or services
using materials subject to input VAT.

4) NO. Atlas doctrine has nothing to do with 120+30 days and whatever
its doctrine was, it was abandoned last June 2007 with the

SECTION 110. (B) Excess Output or Input Tax. - If at the end of any taxable quarter the
output tax exceeds the input tax, the excess shall be paid by the VAT-registered person. If
the input tax exceeds the output tax, the excess shall be carried over to the succeeding
quarter or quarters. Any input tax attributable to the purchase of capital goods or to zerorated sales by a VAT-registered person may at his option be refunded or credited against
other internal revenue taxes, subject to the provisions of Section 112.

pronouncement in Mirant. May refers to the choice of the taxpayer

on whether they would like to file an appeal or not.
o The Atlas doctrine, which held that claims for refund or credit of input
VAT must comply with the two-year prescriptive period under Section

MONTERO // 3A TAX DIGESTS

229, should be effective only from its promulgation on 8 June

2007 until its abandonment on 12 September 2008 in Mirant.
o Reckoning period is the date of payment of the output

5) NO. The RMC 49-03 clarifies that the filing of judicial claims does not
divest the CIR of his jurisdiction to decide on administrative claims.
o There is nothing in RMC 49-03 8 that states, expressly or impliedly, that

VAT
Any payment of output VAT BEFORE Atlas follows the

a judicial claim with the CTA. RMC 49-03 merely authorizes the BIR to

verba legis rule of Section 112(A).

Payment AFTER Atlas also follows the verba legis rule

of Mirant doctrine, which is basically Section 112(A).

o As mentioned, Atlas has no application when it comes to the 120+30

has filed its judicial claim.

o PURPOSE: The internal administrative evaluation of the

the taxpayer need not wait for the 120-day period to expire before filing
continue processing the administrative claim even after the taxpayer

day periods. The 120+30 day rule was first raised in Aichi, which

taxpayers claim must necessarily continue to enable the

adopted the verba legis rule in holding that the 120+30 day periods

BIR to oppose intelligently the judicial claim or, if the

are mandatory and jurisdictional.

o This means that a judicial claim can only be filed after

facts and the law warrant otherwise, for the BIR to

concede to the judicial claim, resulting in the termination

the lapse of said periods.

o When Section 112(C) states that "the taxpayer affected may, within

of the judicial proceedings.

o The expiration of the 120-day period cannot operate to divest the

thirty (30) days from receipt of the decision denying the claim or after

Commissioner of his jurisdiction to decide an administrative

the expiration of the one hundred twenty-day period, appeal the

claim

decision or the unacted claim with the Court of Tax Appeals," the law

120-day

mandatory

period,

unless the

apply as expressly recognized in Section 246 of the Tax Code.

uses the word "may." The word "may" simply means that the

6) YES from 10 December 2003 up to its reversal by this Court

in Aichi on 6 October 2010. BIR Ruling No. DA-489-03 is a general

expiration of the 120 days, the taxpayer can file immediately a petition

interpretative rule and the Commissioner cannot then question the

for review. Now, the VAT system adopts a 30 day rule after the 120

CTAs jurisdiction and equitable estoppel has set in.

days.
o

the

Commissioner has clearly given cause for equitable estoppel to

does not make the 120+30 day periods optional just because the law
taxpayer may or may not appeal.
o The old rule when it comes to judicial appeals is that before the

within

PURPOSE: The 30-day period was adopted precisely

to do away with the old rule, so that under the VAT
System the taxpayer will always have 30 days to file
the judicial claim even if the Commissioner acts
only on the 120th day, or does not act at all during
the 120-day period.

RMC 49-03 - In cases where the taxpayer has filed a Petition for Review with the Court
of Tax Appeals involving a claim for refund/TCC that is pending at the administrative agency
(either the Bureau of Internal Revenue or the One- Stop Shop Inter-Agency Tax Credit and
Duty Drawback Center of the Department of Finance), the administrative agency and the
court may act on the case separately.

MONTERO // 3A TAX DIGESTS

o To recall, BIR Ruling No. DA-489-03 expressly states that the

"taxpayer-claimant need not wait for the lapse of the 120-day

original jurisdiction to interpret tax laws,

period before it could seek judicial relief with the CTA by way of

taxpayers acting in good faith should not be

Petition for Review."

o There is no dispute that the 120-day period is mandatory and
jurisdictional. There are, however, two exceptions to this rule.
o The first exception is if the Commissioner, through a

made

suffer

for

adhering

general

interpretative rules of the Commissioner

o BIR Ruling No. DA-489-03 is a general interpretative rule because it
was a response to a query made, not by a particular taxpayer, but by a

specific ruling, misleads a particular taxpayer to

government agency tasked with processing tax refunds and credits,

prematurely file a judicial claim with the CTA.

Such specific ruling is applicable only to such

that is, the One Stop Shop Inter-Agency Tax Credit and Drawback

particular taxpayer.
Second exception is where the Commissioner, through a
general interpretative rule issued under its power in
Section 4 of the Tax Code (power of the Commissioner
to interpret laws relating to tax and issue regulations),
misleads all taxpayers into filing prematurely judicial
claims with the CTA.
Commissioner cannot then question the CTAs
jurisdiction and equitable estoppel has set in as

Center of the Department of Finance.

o Thus, all taxpayers can rely on BIR Ruling No. DA-489-03 from the
time of its issuance on 10 December 2003 up to its reversal by this
Court in Aichi on 6 October 2010, where this Court held that the
120+30 day periods are mandatory and jurisdictional.
o However, BIR Ruling No. DA-489-03 cannot be given retroactive effect
for four reasons:
o First, it is admittedly an erroneous interpretation of the
o

expressly authorized under Section 246 of the

Tax Code .
o

the correct interpretation of the law;

Third, prior to its issuance, no taxpayer can claim that it
was misled by the BIR into filing a judicial claim

Sec. 246. Non-Retroactivity of Rulings. Any revocation, modification or reversal of any

of the rules and regulations promulgated in accordance with the preceding Sections or
any of the rulings or circulars promulgated by the Commissioner shall not be given
retroactive application if the revocation, modification or reversal will be prejudicial to
the taxpayers, except in the following cases:
(a) Where the taxpayer deliberately misstates or omits material facts from his return or any
document required of him by the Bureau of Internal Revenue;
(b) Where the facts subsequently gathered by the Bureau of Internal Revenue are materially
different from the facts on which the ruling is based; or
(c) Where the taxpayer acted in bad faith.

law;
Second, prior to its issuance, the BIR held that the 120day period was mandatory and jurisdictional, which is

Since the Commissioner has exclusive and

prematurely; and
Fourth, a claim for tax refund or credit, like a claim for

tax exemption, is strictly construed against the taxpayer.

o Given its non-retroactivity, San Roque, cannot benefit from BIR Ruling
No. DA-489-03 because it filed its judicial claim prematurely on 10
April 2003, BEFORE the issuance of BIR Ruling No. DA-489-03 on 10
December 2003.

MONTERO // 3A TAX DIGESTS

o Taganito, however, filed its judicial claim with the CTA on 14 February

8) NO. Section 4.106-2(c) of Revenue Regulations No. 7-95 did not

2007, AFTER the issuance of BIR Ruling No. DA-489-03 on 10

allow premature filing of judicial claims. Even assuming the

December 2003.
o Philexs situation is not a case of premature filing of its judicial claim

contrary, Section 4.106-2(c), a mere administrative issuance,

but of late filing, indeed very late filing.

becomes inconsistent with Section 112(D), a later law. Obviously,

the later law prevails over a prior inconsistent administrative

7) NO. None of these five cases mention, cite, discuss, rule or even

issuance.
o (This issue is pertinent since San Roque claims that the case is one

hint that compliance with the 120-day mandatory period is

under the 1977 Tax Code which was amended by Section 4.106-2(c)

inconsequential as long as the administrative and judicial claims are

of Revenue Regulations No. 7-95. San Roque assumes that the old

filed within the two-year prescriptive period.

o In CIR v. Toshiba Information Equipment (Phils.), Inc., the issue was

law allows premature filing)

o Section 4.106-2(c) of Revenue Regulations No. 7-95, by its own

whether any output VAT was actually passed on to Toshiba that it

express terms, applies only if the taxpayer files the judicial claim

could claim as input VAT subject to tax credit or refund.

o In Intel Technology Philippines, Inc. v. CIR, the Court stated: "The

"after" the lapse of the 60-day period, a period with which San Roque

issues to be resolved in the instant case are (1) whether the absence
of the BIR authority to print or the absence of the TIN-V in petitioners

mandatory and jurisdictional.

o Under the 1977 Tax Code (Yes, the OLD pa cinite ng court just to

export sales invoices operates to forfeit its entitlement to a tax

prove na luma na yung mandatory periods even before we had the

refund/credit of its unutilized input VAT attributable to its zero-rated

120 days!)
o

sales; and (2) whether petitioners failure to indicate "TIN-V" in its

sales invoices automatically invalidates its claim for a tax credit

failed to comply. Under Section 4.106-2(c), the 60-day period is still

(d) Period within which refund or tax credit of input tax

shall be made - In proper cases, the Commissioner shall

certification..
o In AT&T Communications Services Philippines, Inc. v. CIR, the Court

grant a refund or issue the tax credit for creditable input

denied the claim for lack of substantiation given that "valid VAT

submission of complete documents in support of the

official receipts, and not mere sale invoices, should have been

application filed in accordance with subparagraphs (a)

submitted.
o In CIR v. Ironcon Builders and Development Corporation was about

and (b) hereof. In case of full or partial denial of the

the issue on the validity for refund of excess creditable VAT withheld.
o In CIR v. Cebu Toyo Corporation, the issue was whether Cebu Toyo

part of the Commissioner to act on the application

was exempt or subject to VAT.

taxes within

sixty

(60)

days from

the

date

claim for tax refund or tax credit, or the failure on the

within the period prescribed above, the taxpayer
affected may, within thirty (30) days from receipt of
the decision denying the claim

or after the

MONTERO // 3A TAX DIGESTS

expiration of the sixty-day period, appeal the

the 1997 Tax Code, not the 1977 Tax Code. Since San Roque filed its

decision or the unacted claim with the Court of Tax

judicial claim before the expiration of the 120-day mandatory and

Appeals.
o Revenue Regulations No. 7-95 (1996)
o However, if no action

jurisdictional period, San Roques claim cannot prosper.

o San Roque cannot also invoke Section 4.106-2(c), which
tax

expressly provides that the taxpayer can only file the

credit/refund has been taken by the Commissioner

judicial claim "after" the lapse of the 60-day period from

the filing of the administrative claim. San Roque filed

Internal

period from

the

claim

Revenue after

the

submission

date

sixty

for
(60)

day

the

its judicial claim just 13 days after filing its

application but before the lapse of the two (2) year

period from the date of filing of the VAT return for
the taxable quarter, the taxpayer may appeal to the
Court of Tax Appeals.
o Base from above, Revenue Regulations No. 7-95 (1996) did not
allow the filing of claims before the lapse of 60 days.
o Section 4.106-2(c) itself expressly states that if, "after
the sixty (60) day period,"
o Even assuming the contrary, Section 4.106-2(c), a mere administrative
issuance, becomes inconsistent with Section 112(D), a later law.
Section 112(D) of the 1997 Tax Code is clear, unequivocal, and
categorical that the Commissioner has 120 days to act on an
administrative claim. The taxpayer can file the judicial claim (1) only
within thirty days after the Commissioner partially or fully denies
the claim within the 120- day period, or (2) only within thirty days

administrative claim.
*Did not include the Dissenting Opinions so that the case wont be too long.
Dissenters: (1) CJ MARIA LOURDES P. A. SERENO, (2) PRESBITERO J.
VELASCO, JR., (3) JOSE C. MENDOZA, and (4) ESTELA M. PERLASBERNABE

NIPPON EXPRESS CORPORATION v. COMMISSIONER OF

INTERNAL REVENUE (Banta)
[GR. No. 196907; March 13, 2013]
Matuto kang maghintay. 120 days lang naman (ang kailangang mag-lapse).
Hindi yung lilipat ka agad sa iba.
Recit-Ready:
Facts: Petitioner Nippon Philippines filed an administrative claim for

from the expiration of the 120- day period if the Commissioner does

refund with the BIR, representing excess input tax attributable to

not act within the 120-day period.

o There can be no dispute that upon effectivity of the 1997 Tax Code on

its effectively zero-rated sales in 2001. The day after it filed in the
BIR, and while its claim was still pending review, it already filed a

1 January 1998, or more than five years before San Roque filed its

petition for review with the CTA, requesting for the issuance of a

administrative claim on 28 March 2003, the law has been clear: the

tax credit certificate.

120- day period is mandatory and jurisdictional. San Roques claim,

having been filed administratively on 28 March 2003, is governed by

The subsequent rulings of the lower courts are as follows:

MONTERO // 3A TAX DIGESTS

CTA First Division: denied petitioner for insufficiency of

claim with the CTA would not only make such petition premature,

evidence

but would also result in the non-acquisition by the CTA of

Upon MR: reversed

jurisdiction to hear the said case.

CTA En Banc: reversed the CTA Amended Decision and

The Court however took into consideration the issuance by the BIR of

denied petitioners claim for lack of merit

Ruling No. DA- 489-03, which expressly stated that the taxpayer need

CTA reversed its decision and affirmed the final decision

not wait for the lapse of the 120-day period before seeking judicial

of the First Division

relief. Because taxpayers cannot be faulted for relying on this

Upon MR by the CIR: the CTA did another reversal and

declaration by the BIR, the Court deemed it reasonable to allow

held that the CTA has no jurisdiction over the petition for

taxpayers to file its judicial claim even before the expiration of the

review because it was filed before the lapse of the 120-

120-day period.

day period accorded to the CIR

SO AGAIN, GENERAL RULE (as laid down by San Roque case):

Issues:

judicial claims filed from January 1, 1998 until the present should

1) WON the CTA has jurisdiction over the instant case

NO
2) WON the petitioners VAT invoices are insufficient proof to

strictly adhere to the 120+30-day period referred to in Section 112

of the NIRC. EXCEPTION: period from December 10, 2003 until
October 6, 2010, during which, judicial claims may be filed even before

support its zero-rated sales

No need to discuss

the expiration of the 120-day period granted to the CIR to decide on

the claim for refund.

Held:
1) NO. Petition is without merit. A simple reading of Section 112(D)
reveals that the taxpayer may appeal the denial or the inaction of
the CIR only within thirty (30) days from receipt of the decision
denying the claim or the expiration of the 120-day period given to
the CIR to decide the claim.
Contrary to petitioners position, the 120+30-day period is indeed
mandatory and jurisdictional from the time of effectivity of R.A. No.
8424, as recently ruled in CIR V. SAN ROQUE POWER CORPORATION.
Thus, the failure to observe the said period before filing a judicial

2) Having thus concluded, the Court sees no need to discuss other

issues which may have been raised in the petition.
Facts:

Petitioner NIPPON EXPRESS (PHILIPPINES) CORPORATION is a

corporation duly organized and registered with the Securities and
Exchange Commission
o Also, it is a VAT-registered entity with the Large Taxpayer District
o

of the BIR
2001: it regularly filed its amended quarterly VAT returns

MONTERO // 3A TAX DIGESTS

April 24, 2003: petitioner filed an administrative claim for refund of

P20,345,824.29 representing excess input tax attributable to its effectively

affirmed the initially struck down Amended Decision of the First Division
o In light of the case of AT&T COMMUNICATIONS SERVICES

zero-rated sales in 2001

April 25, 2003: pending review by the BIR, petitioner filed a petition for

PHILIPPINES, INC. V. COMMISSIONER

OF INTERNAL

REVENUE, where

review with the CTA, requesting for the issuance of a tax credit certificate

it was ruled that Section 113 does not distinguish between a

in the amount of P20,345,824.29

o CTA First Division: denied the petition for insufficiency of

sales invoice and an official receipt, the CTA found petitioners

evidence
Upon MR, CTA First Division: reversed its decision and ordered

of tax credit certificate representing its excess or unutilized input

respondent CIR to issue a tax credit certificate in favor of

sales invoices to be acceptable proof for the refund or issuance

VAT
CIR then filed a motion for reconsideration, arguing that a sales receipt

petitioner, representing excess or unutilized input tax for the

and a sales invoice are not the same, and that the CTA has no jurisdiction

second-fourth quarters of 2001

As to the TIMELINESS OF THE CLAIM:
CTA First Division recognizes that the claim was

over the petition for review because it was filed before the lapse of the
120-day period accorded to the CIR
o CTA granted CIRs MR and once again reversed its decision,

premature because pursuant to Section 112(D) of the

NIRC, petitioner should have made its appeal with the

(sellers proof of sale) and a VAT receipt (buyers best evidence

denying the claim, OR after the expiration of the 120-day

of payment) should not be confused as referring to the same

period without action from the CIR

However, since the CIR did not register any objection

thing

deemed waived
June 11, 2010: CTA En Banc reversed and set aside the Amended
Decision and Resolution of the First Division; denied petitioners claim for

Issues:
1) WON the CTA has jurisdiction over the instant case
NO
2) WON the petitioners VAT invoices are insufficient proof to support

lack of merit
o According to the CTA En Banc:
The sales invoices issued by petitioner were insufficient

dismissing the petition for lack of jurisdiction

Also, KEPCO PHILIPPINES CORPORATION V. CIR: a VAT invoice

CTA 30 days from the receipt of the decision of the CIR

with regard to the timeliness of the claim, it has been

September 22, 2010: CTA En Banc reversed its own decision, and

its zero-rated sales

No need to discuss

to establish its zero-rated sale of services;

Without the proper VAT official receipts issued to tis

Held/Ratio: The Court finds the petition WITHOUT MERIT.

clients, the payments received by petitioner could not

qualify for zero-rating for VAT purposes

NO. Petitioner is mistaken. A simple reading of Section 112(D)

reveals that the taxpayer may appeal the denial or the inaction of

MONTERO // 3A TAX DIGESTS

the CIR only within thirty (30) days from receipt of the decision

acquisition by the CTA of jurisdiction to hear the said

denying the claim or the expiration of the 120-day period given to

the CIR to decide the claim.
O Petitioner contends that:
Non-exhaustion of remedies is not a jurisdictional defect;
CIR failed to seasonably object therefore, it is deemed

waived;
It cannot

faulted

for

relying

prevailing

petitioner complied with the said time frame may be breached at any
stage, even on appeal
Jurisdiction cannot be waived because it is conferred by law
and is not dependent on the consent or objection or the acts

CTA

jurisprudence requiring that both administrative and judicial

claims for refund be filed within the two (2) years from the
O

case
Because the 120+30 day period is jurisdictional, the issue of whether

or omissions of the parties or any one of them

The Court however took into consideration the issuance by the BIR of
Ruling No. DA- 489-03, which expressly stated that the taxpayer need

date of the filing of the return and the payment of the tax due
Section 112(D) (now Subpar. 6) of the NIRC is clear:

not wait for the lapse of the 120-day period before seeking judicial
relief

(D) Period within which Refund or Tax Credit of Input Taxes shall be Made. In

Because taxpayers cannot be faulted for relying on this

declaration by the BIR, the Court deemed it reasonable to

proper cases, the Commissioner shall grant a refund or issue the tax credit

allow taxpayers to file its judicial claim even before the

certificate for creditable input taxes within one hundred twenty (120) days from
the date of submission of complete documents in support of the application
filed in accordance with Subsections (A) and (B) hereof.

expiration of the 120-day period

This exception is to be observed from December 10, 2003
until its REVERSAL by AICHI in October 6, 2010
In the case of AICHI, the Court made a definitive

In case of full or partial denial of the claim for tax refund or tax credit, or the
failure on the part of the Commissioner to act on the application within the

statement that the failure of a taxpayer to wait for the

period prescribed above, the taxpayer affected may, within thirty (30) days
from the receipt of the decision denying the claim or after the expiration

decision of the CIR or the lapse of the 120-day

of the one hundred twenty day-period, appeal the decision or the unacted

period will render the filing of the judicial claim with

claim with the Court of Tax Appeals. (Emphasis Supplied)

Contrary to petitioners position, the 120+30-day period is indeed

mandatory and jurisdictional from the time of effectivity of R.A. No.
8424, as recently ruled in CIR V. SAN ROQUE POWER CORPORATION
Thus, failure to observe the said period before filing a
judicial claim with the CTA would not only make such
petition premature, but would also result in the non-

the CTA premature

SO AGAIN, GENERAL RULE (as laid down by San Roque case):
judicial claims filed from January 1, 1998 until the present should
strictly adhere to the 120+30-day period referred to in Section 112
of the NIRC

EXCEPTION: period from December 10, 2003 until October

6, 2010, during which, judicial claims may be filed even
before the expiration of the 120-day period granted to the CIR
to decide on the claim for refund

MONTERO // 3A TAX DIGESTS

disallowed on the ground that the use of said business name by petitioner
2) Having thus concluded, the Court sees no need to discuss other issues

was never approved by the Securities and Exchange Commission (SEC).

which may have been raised in the petition.

BWC filed its Petition for review with the CTA En Banc. However, the CTA

BONIFACIO WATERS v. CIR (Bello)

En Banc, affirmed in toto the assailed Decision and Resolution of the CTA

[GR. No. 175142; July 22, 2013

Second Division

Taxpayers must show satisfaction of all the documentary and evidentiary

requirements before an administrative claim for refund or tax credit will be

Issue: WON the CTA En Banc erred in not granting petitioners claim

granted

for refund or issuance of a tax credit certificate in the amount

of P65,642,814.65? NO! (hindi siya nagkamali)

Recit-Ready:
Facts: Bonifacio Water Corporation (BWC) is a domestic corporation

Held:

WHEREFORE, premises considered, the instant petition is

engaged in the collection, purification and distribution of water. BWC duly

DENIED. The Court of Tax Appeals En Banc Decision dated June

filed with the BIR its quarterly VAT returns for the year 1999-2000.

26, 2006, and Resolution dated October 19, 2006, are hereby
AFFIRMED.

For said period, BWC alleges that its input VAT included, among others,
input

VAT

paid

purchases

capital

goods

amounting

to P65,642,814.65.

NO! The requisite that the receipt be issued showing the name, business
style, if any, and address of the purchaser, customer or client is precise so
that when the books of accounts are subjected to a tax audit examination,

These purchases supposedly pertain to payment to contractors in

all entries therein could be shown as adequately supported and

connection with the construction of petitioners Sewage Treatment Plant,

proven as legitimate business transactions. The absence of official

Water and Waste System, and Water Treatment Plant. Hence, BWC filed a

receipts issued in the taxpayers name is tantamount to non-

claim for refund amounting P65,642,814.65 representing unutilized input

compliance with the substantiation requirements provided by law.

VAT on capital goods purchased for the period beginning the 4th quarter of
1999 up to the 4th quarter of 2000.

Thus, the change of petitioners name to "Bonifacio GDE Water

The next day, petitioner filed its Petition for Review with the Court of Tax

and the issuance of official receipts under that name which were

Appeals (CTA) and rendered a Decision partially granting petitioners claim

for refund in the reduced amount of P40,875,208.64 on the basis that the
official receipts under the name "Bonifacio GDE Water Corporation" were

Corporation," being unauthorized and without approval of the SEC,

presented to support petitioners claim for tax refund, cannot be
used to allow the grant of tax refund or issuance of a tax credit
certificate in petitioners favor. The absence of official receipts issued in

MONTERO // 3A TAX DIGESTS

its name is tantamount to noncompliance with the substantiation

of P40,875,208.64. (Partially granting lang so hindi buong 65k yung allow

requirements provided by law and, hence, the CTA En Bancs partial grant

na refund)

of its refund on that ground should be upheld.

CTA Second Division held that an examination of the various official receipts
presented by petitioner, to support its purchases for capital goods, shows

Facts:

Bonifacio Water Corporation (BWC) is a domestic corporation engaged in

the collection, purification and distribution of water. It is registered with the

official receipts under the name "Bonifacio GDE Water Corporation" were

with VAT Registration/Taxpayer Identification No. 201-403-657-000.

BWC duly filed with the BIR its quarterly VAT returns for the 4th

was never approved by the Securities and Exchange Commission (SEC).

2000, and 4th quarter of 2000, declaring the following information:

For said period, BWC alleges that its input VAT included, among
others, input VAT paid on purchases of capital goods amounting
to P65,642,814.65. These purchases supposedly pertain to payment to
contractors in connection with the construction of petitioners Sewage

Treatment Plant, Water and Waste System, and Water Treatment Plant.
On January 22, 2002, petitioner filed with Revenue District Office No. 44
Pateros and Taguig, Revenue Region No. 8 of the BIR,

administrative claim for refund or issuance of a tax credit certificate

in the amount of P65,642,814.65 representing unutilized input VAT
on capital goods purchased for the period beginning the 4th quarter

overhead, cannot be considered as capital goods. Further, it ruled that the

Bureau of Internal Revenue (BIR) as a value-added tax (VAT) taxpayer,

quarter of 1999, 1st quarter of 2000, 2nd quarter of 2000, 3rd quarter of

that some of its purchases, such as rental, management fees and direct

disallowed on the ground that the use of said business name by petitioner
(Ito yung wherefore ni CTA Second Division, medyo important yung decision
niya lalo na yung hindi approve yung new alleged business name ni BWC)

BWC thereafter filed its petition for review with the CTA En Banc arguing
that it has presented substantial evidence that proves its input VAT on
purchases of capital goods from the 4th quarter of 1999 to the 4th quarter
of 2000, as well as the fact that petitioner and "Bonifacio GDE
Corporation" are one and the same entity. (Dahil hindi siya makuntento sa
45k, nag appeal siya sa CTA En Banc

In a Decision dated June 26, 2006, the CTA En Banc affirmed in toto the
assailed Decision and Resolution of the CTA Second Division.

of 1999 up to the 4th quarter of 2000. (In short, ito basis niya to claim

Issue:

refund or issuance of tax credit)

The next day, petitioner filed its Petition for Review with the Court of Tax

WON the CTA En Banc erred in not granting petitioners claim for
refund or issuance of a tax credit certificate in the amount

Appeals (CTA), to toll the running of the two-year prescriptive period.

of P65,642,814.65?
NO

(Dahil alam niya mag prescribe na, nagfile sa CTA galing niya eh) On
March 29, 2005, the CTA Second Division rendered a Decision partially
granting petitioners claim for refund in the reduced amount

You may opt not to read this part:

PETITIONERs ARGUMENTS
1.

That Non-compliance with the

invoicing requirements under

RESPONDENTs ARGUMENTS
A.

that the instant petition raises

purely questions of fact which is

MONTERO // 3A TAX DIGESTS

the 1997 Tax Code does not

not allowed under Rule 45 of the

inter alia, that the input taxes

authority and to be construed

automatically

the

Rules of Court. He highlights the

claimed as refund were duly

strictissimi juris against the entity

denial of a claim for refund or

result

fact that the issue of whether or

supported by valid VAT invoices

claiming the exemption.

tax credit when the same is

not petitioner was able to present

supported

substantial

substantial evidence to prove and

and/or receipts.
that the CTA imposed an overly

evidence. It contends that the

support its claim for tax refund or

strict standard of evidence in

CTA En Banc erred in sustaining

tax credit calls for this Court to

disallowing petitioners invoices

the ruling that petitioner is not

review

the

bearing the name "Bonifacio GDE

entitled to a refund of the input

evidence to enable it to determine

Water Corporation." It claims that

VAT evidenced by official receipts

and resolve the issues raised by

the denial of the claim in its

in the name of "Bonifacio GDE

petitioner.

entirety based purely on technical

Water Corporation.
that the CTA erred in failing to

and

evaluate

all

grounds

deprives

that the CTA En Banc committed

petitioner of a right granted by law

properly apply the definition of

no error in not applying the rules

and

capital goods and insists that

regarding

deprivation of its property.

services

the

since no judicial admission was

construction and installation of

made by or was attributable to

capital assets and goods should

respondent,

be included in the cost of capital

pleadings or in the course of the

goods

trial proceedings. He argues that

incurred

for

purposes

judicial

admissions,

either

admission

made

the

constitutes

undue

Held/Ratio: WHEREFORE, premises considered, the instant petition is

DENIED. The Court of Tax Appeals En Banc Decision dated June 26, 2006,
and Resolution dated October 19, 2006, are hereby AFFIRMED.

determining the proper amount of

the

refundable input VAT.

subordinate BIR official in support

NO. The change of name to Bonifacio GDE Corporation being

of the course of action which he

unauthorized and without approval from the Securities and Exchange

had proposed or submitted for

approval by his superior cannot by
any stretch of imagination be
considered an admission, much

Commission, petitioner cannot now seek for a refund of input taxes,

which are supported by receipts under that name. (Pwede ka naman
bigyan ng refund eh, yung receipt mo lang sa iba na nakapangalan)

less a judicial admission, of the

unduly

that

respondent

made

latter.
that the CTA En Banc did not err

"informal judicial admission" and

in using stricter rules of evidence

partially recognized its claims for

in cases involving claims for tax

excess input VAT on purchases of

refund or tax credit as the same

capital

goods

are

District

No.

memorandum

when
44

Revenue
issued

acknowledging,

the

nature

tax

exemptions and are regarded as

derogation

sovereign

The requisite that the receipt be issued showing the name, business
style, if any, and address of the purchaser, customer or client is
precise so that when the books of accounts are subjected to a tax
audit examination, all entries therein could be shown as
adequately supported and proven as legitimate business
transactions. The absence of official receipts issued in the

MONTERO // 3A TAX DIGESTS

taxpayers name is tantamount to non-compliance with the

substantiation requirements provided by law and, hence, the CTA En

substantiation requirements provided by law.

Petitioner cannot raise the argument that, "non-compliance with the

Bancs partial grant of its refund on that ground should be upheld.

invoicing requirements under the 1997 NIRC, as amended, does not

automatically result in the denial of a claim for refund or tax credit
when the same is supported by substantial evidence" and that, "In civil
cases, such as claims for refund, strict compliance with technical rules
O

of evidence is not required.

Moreover, a mere preponderance of evidence will suffice to

Also, petitioners allegation that some of the disallowed input taxespaid on

services related to the construction of petitioners Waste Water Treatment
and Water Sewerage Distribution Networks, should be included as part of its
capital goods, must fail.
o

goods since "capital goods" is defined as: "Capital goods or

instant petition. Taxpayers claiming for a refund or tax credit

properties" refer to goods or properties with estimated useful life

certificate must comply with the strict and mandatory invoicing

greater than one year and which are treated as depreciable assets

and accounting requirements provided under the 1997 NIRC, as

under Section 29(f), used directly or indirectly in the production or

amended, and its implementing rules and regulations. Rules and

sale of taxable goods or services.

Had petitioner intended the aforementioned itemized expenses

ignored or to be taken for granted, but are strictly adhered to for they

to be part of Property, Plant & Equipment, then it should have

are developed from the law itself.

From the foregoing, it is clear that petitioner must show satisfaction of

recorded the same to the foregoing specific accounts. Except

all the documentary and evidentiary requirements before an

do not fall within the definition of capital goods pursuant to Section

administrative claim for refund or tax credit will be granted. Perforce,

4.106-1(b) of Revenue Regulations No. 7-95.

the taxpayer claiming the refund must comply with the invoicing and

for the account "Construction in Progress," the other expense items

accounting requirements mandated by the Tax Code, as well as the

Only real accounts provided above are to be considered as capital

justify the grant of a claim," in addition to its first ground in the

regulations with regard to procedures are implemented not to be

OTHERS (you may opt not to read this)

aside the conclusions reached by the CT A which, by the very

revenue regulations implementing them.

Thus, the change of petitioners name to "Bonifacio GDE Water

nature of its function of being dedicated exclusively to the

resolution of tax problems, has accordingly developed an

Corporation," being unauthorized and without approval of the

expertise on the subject, unless there has been an abuse or

SEC, and the issuance of official receipts under that name which
were presented to support petitioners claim for tax refund,
cannot be used to allow the grant of tax refund or issuance of a
tax credit certificate in petitioners favor. The absence of official
receipts issued in its name is tantamount to noncompliance with the

As a final point, it is doctrinal that the Court will not lightly set

improvident exercise of authority.

In fact, in Barcelon, Roxas Securities, Inc. v. Commissioner of

Internal Revenue, this Court held that it accords the findings of fact
by the CT A with the highest respect. It ruled that factual findings
made by the CTA can only be disturbed on appeal if they are

MONTERO // 3A TAX DIGESTS

supported by substantial evidence or there is a showing of gross

prescriptive periods under the Tax Code.

error or abuse on the part of the Tax Court. In the absence of any
clear and convincing proof to the contrary, this Court must presume
o

Held:

The claims of respondent GST Philippines, Inc. for refund or tax

that the CT A rendered a decision which is valid in every respect.

credit for unutilized excess input VAT for the four quarters of

In the present case, no cogent reason exists for this Court to deviate

taxable year 2004, as well as the first quarter of taxable year

from this well-entrenched principle, since the CT A En Bane neither

2005 are hereby DENIED for being filed beyond the prescriptive

abused its authority nor committed gross error in partially denying

period, while the claims for refund for the second and third

petitioner's refund claim.

quarters of taxable year 2005 are GRANTED. Accordingly, the

Commissioner of Internal Revenue is ordered to refund or, in the

CIR v. GST PHILIPPINES, INC. (Bugay)

alternative, to issue a tax credit certificate to respondent GST

[GR. No. 190872; October 17, 2013]

Philippines, Inc. corresponding only to the amount representing

120 + 30- day period mandatory and jurisdictional

unutilized excess input VAT for the second and third quarters of
taxable year 2005 out of the total amount of P27,369,114.36
awarded by the CTA.

Recit-Ready:
Facts: Respondent GST is a VAT registered domestic corporation
primarily engaged in steel and iron products. During taxable years

Facts:

2004-2005, GST filed claimed for unutilized excess input VAT

GST is a corporation duly organized and existing under the laws of the

attributable to its zero rated sales. For failure of CIR to act on its

Philippines, and primarily engaged in the business of manufacturing,

administrative claims, GST filed for a petition for review before the

processing, selling, and dealing in all kinds of iron, steel or other metals.
o Duly registered VAT enterprise, which deals with companies

CTA. The CTA granted the petition. CIR filed an MR but was
denied. In a petition for review before the CTA En Banc, CIR
raised that the appeal before the CTA was filed beyond the

registered with:
The Board

administrative and judicial claims are filed within the two-year

prescriptive period; and that compliance with the 120-day and 30day periods under Section 112 (D) of the Tax Code is not
mandatory.
Issue: WON GSTs action for refund has complied with the

Investments

(BOI),

whose

manufactured products are 100% exported to

reglementary period. GST asserts that under Section 112 (A) of

the Tax Code, the prescriptive period is complied with if both the

foreign countries; and

The Philippine Economic Zone Authority (PEZA)
Sales made by a VAT-registered person to
a PEZA-registered entity are considered
exports to a foreign country subject to a
zero rate.

MONTERO // 3A TAX DIGESTS

During the taxable year, GST filed Quarterly VAT returns showing its
zero-rated sales:
Period
1st Quarter 2004
2nd Q. 2004
3rd Q. 2004

Date of Filing
April 16, 2004
July 15, 2004
October
15,

Zero-Rated Sales
P 77,687,420.54
53, 737,063.05
74,280,682.00

4 Q. 2004

2004
January

104,633,604.23

1st Q. 2005

2005
April 25, 2005

37,742,969.02

2nd Q. 2005
3rd Q. 2005

July 19, 2005

October
26,

56,133,761.00
51,147,677.60

11,

2005
Claiming unutilized excess input VAT in the total amount of
P32,722,109.68 attributable to the foregoing zero-rated
sales, GST filed before the BIR separate claims for refund.
Period

Date of Filing Admin. Claim

for Refund
1st Quarter 2004
June 9, 2004
nd
2 Q. 2004
August 12, 2004
3rd Q. 2004
February 18, 2005
th
4 Q. 2004
February 18, 2005
1st Q. 2005
May 11, 2005
nd
2 Q. 2005
November 18, 2005
rd
3 Q. 2005
November 18, 2005
For failure of the CIR to act on it administrative claims, GST filed a
petition for review before the CTA on March 17, 2006.

Issue:
WON GSTs action for refund has complied with the prescriptive
periods under the Tax Code. No and Yes.
Held/Ratio: Petition is PARTLY GRANTED. The Decision dated October 30,
2009 of the Court of Tax Appeals En Banc in C.T.A. EB No. 484, affirming
the Decision dated January 27, 2009 of the CTA First Division in C.T.A. Case
No. 7419, is AFFIRMED with10 MODIFICATION. The claims of respondent
10

Section [Link] or Tax Credits of Input Tax.

(A) Zero-rated or Effectively Zero-rated Sales. Any VAT-registered person, whose sales
are zero- rated or effectively zero-rated may, within two (2) years after the close of the
taxable quarter when the sales were made, apply for the issuance of a tax credit
certificate or refund of creditable input tax due or paid attributable to such sales, except
transitional input tax, to the extent that such input tax has not been applied against output
tax: . . . . (Emphasis supplied)
xxx xxx xxx
(D) Period within which Refund or Tax Credit of Input Taxes shall be Made. In proper
cases, the Commissioner shall grant a refund or issue the tax credit certificate for creditable
input taxes within one hundred twenty (120) days from the date of submission of
complete documents in support of the application filed in accordance with Subsections (A)
and (B) hereof.
In case of full or partial denial of the claim for tax refund or tax credit, or the failure on the
part of the Commissioner to act on the application within the period prescribed above, the

MONTERO // 3A TAX DIGESTS

GST Philippines, Inc. for refund or tax credit for unutilized excess input

30-day period always available to the taxpayer, the taxpayer

VAT for the four quarters of taxable year 2004, as well as the first

can no longer file a judicial claim for refund or tax credit of

quarter of taxable year 2005 are hereby DENIED for being filed beyond

unutilized excess input VAT without waiting for the

the prescriptive period, while the claims for refund for the second and

Commissioner to decide until the expiration of the 120-day

third quarters of taxable year 2005 are GRANTED.

period.

Failure to comply with the 120-day waiting

period

violates

doctrine

exhaustion

Refund or tax credit of unutilized excess input VAT has been

administrative remedies and renders the petition

allowed as early as in the Original VAT Law EO 273. Since

premature and thus without a cause of action, with the

GST's claims for refund covered the periods before the

effect that the CTA does not acquire jurisdiction over

effectivity of RA 9337, the old provision on VAT refund,

the

specifically Section 112, as amended by RA 8424, shall apply.

The claims filed for the four quarters of taxable year 2004, as well as

the taxpayer's petition.

In CIR v. San Roque Power Corporation, the Court held that
BIR Ruling No. DA-489-03 dated December 10, 2003

the first quarter of taxable year 2005, had already prescribed. While

provided a valid claim for equitable estoppel under Section

those of the second and third quarters of taxable year 2005 were

246 of the Tax Code. BIR Ruling No. DA-489-03 expressly

prematurely filed.
The Court held in Cir v. Aichi Forging Company of Asia, Inc., that the

states that the taxpayer-claimant need not wait for the

two-year prescriptive period applies only to administrative claims and

relief with the CTA by way of Petition for Review.

There are two exceptions to this rule:
First, if the Commissioner, through a

not to judicial claims. Further, it ruled that the 120-day and 30-day
periods are mandatory.
o The second paragraph of Section 112(D) [now Section

lapse of the 120-day period before it could seek judicial

specific

misleads

particular

taxpayer to prematurely file a judicial claim

decision is issued by the CIR before the lapse of the

with the CTA. Such specific ruling is

120-day period; and (2) when no decision is made after

applicable only to such particular taxpayer.

Second, where the Commissioner, through

the 120-day period. In both instances, the taxpayer has

ruling,

112(C)] of the NIRC envisions two scenarios: (1) when a

30 days within which to file an appeal with the CTA.

The taxpayer will always have 30 days to file the judicial

a general interpretative rule issued under

claim even if the Commissioner acts only on the 120th day,

taxpayer into filing prematurely judicial

or does not act at all during the 120-day period. With the

claims with the CTA.

In these cases, the Commissioner cannot be

taxpayer affected may, within thirty (30) days from the receipt of the decision denying
the claim or after the expiration of the one hundred twenty day-period, appeal the
decision or the unacted claim with the Court of Tax Appeals. (Emphasis supplied)

Section 4 of the Tax Code, misleads all

allowed to later on question the CTAs assumption

MONTERO // 3A TAX DIGESTS

of jurisdiction over such claim since equitable

The Court further emphasized that tax refunds partake of the nature of

estoppel has set in as expressly authorized under

tax exemptions which are a derogation of the power of taxation of the

Section 246 of the Tax Code.

BIR Ruling No. DA-489-03 was classified in San Roque as a

State. Consequently, they are construed strictly against a taxpayer and

general interpretative rule having been made in response to a

entitlement to a refund, but also its compliance with the prescribed

query by a government agency tasked with processing tax refunds

liberally in favor of the State. Thus, a taxpayer must prove not only its
procedures.

and credits the One Stop Shop Inter-Agency Tax Credit and
Drawback Center of the Department of Finance.
o Therefore, GST can benefit from BIR Ruling No. DA-489-03
with respect to its claims for refund of unutilized excess
input VAT for the second and third quarters of taxable year
2005, which were filed before the CIR on November 18,
2005, but elevated to the CTA on March 17, 2006 before
the expiration of the 120-day period. BIR Ruling No. DA489-03 effectively shielded the filing of GSTs judicial claim
from the vice of prematurity.

Taxable Period
1st Q. 2004
2nd Q. 2004
3rd Q. 2004
4th Q. 2004
1st Q. 2005
2nd Q. 2005
3rd Q. 2005
It can be observed from

Remarks
Filed Late
Filed Late
Filed Late
Filed Late
Filed Late
Prematurely Filed
Prematurely Filed
the Courts application

Action on Claim
DENY
DENY
DENY
DENY
DENY
GRANT
GRANT
of the 120+ 30-day

CIR v. MINDANAO II GEOTHERMAL PARTNERSHIP (Caraan)

[GR. No. 191498; January 15, 2014]
Taxpayer may file his application for refund/tax credit within 2 years from the
close of the taxable quarter when the relevant sales were made.
CIR has 120 days after the application is filed to act on it.
Upon denial of the claim/inaction of the CIR after 120 days, the taxpayer has
30 days to appeal to the CTA
Recit-Ready:
Facts: Mindanao II is engaged in the business of power generation and
sale of electricity to NAPOCOR. It filed its Quarterly VAT Returns
for the 2nd-4th Quarters of 2004 then filed an application for the
refund/credit of accumulated unutilized creditable input taxes on
October 6, 2005. Pursuant to Section 112(D) of the 1997 Tax
Code, the CIR had 120 days (or until February 3, 2006) to act on
such application; however, this remained unresolved.

period to GSTs claims, the 120-day period is uniformly reckoned

Such inaction from the CIR can be treated as a denial of the claim

from the date of the filing of the administrative claims.

The reckoning date of the 120-day period commenced

for refund/tax credit; thus, the provision states that the taxpayer

simultaneously with the filing of the administrative claims when

the CTA within 30 days because it believed that the prescriptive

GST was presumed to have attached the relevant document to

period was two years to file an appeal.

support its applications for refund or tax credit.

has 30 days to appeal to the CTA. Mindanao II did not appeal to

MONTERO // 3A TAX DIGESTS

Issues:

attributable to the zero-rated sales and the input taxes had

1) WON Mindanao II filed its claim on time by relying on the two-year

prescriptive period for filing an application for refund or credit of
unutilized input VAT
2) WON Mindanao II filed its appeal to the CTA on time by relying on the

not been applied against output tax

Pursuant to Section 112(D) of the 1997 Tax Code, petitioner CIR had a
period of 120 days (or February 3, 2006) to act on the claim of Mindanao
II; however, it remained unresolved.
o Under the same provision; Mindanao II could treat such

two-year period as well

inaction as a denial of its claim, and thus, it can file an

Held:
1) YES. The claim for refund / tax credit can be filed with the CIR within
two years from the close of the taxable quarter when the relevant
sales were made. (So Mindanao II had two years from the close of the

appeal to the CTA after 30 days (or March 5, 2006)

o But Mindanao II did not file an appeal within such period
Mindanao II believed that the judicial claim (the appeal to the CTA) must
be filed within two years and so it filed its Petition for Review to the CTA

2nd, 3rd, and 4th quarters of 2004 to file its claim to the CIR. But it filed

on July 21, 2006.

o While this was pending, the SC promulgated Atlas

early naman, so yeah)

2) NO. (Dito na nagkamali and nawalan si Mindanao II) When the CIR

Consolidated Mining and Development Corporation v. CIR

failed to act on Mindanao IIs application within 120 days, Mindanao II

(Atlas) and held that the two-year prescriptive period for

only had a period of 30 days to appeal to the CTA. It did not have the

the filing of a claim for an input VAT refund or credit is to be

full two-year period as the two-year period is only for when the

reckoned from the date of filing of the corresponding

taxpayer could file his claim for refund/tax credit.

Facts:

Respondent Mindanao II is a partnership engaged in the business of

power generation and sale of electricity to the National Power Corporation

quarterly VAT return and payment of the tax.

The CTA rendered its decision and ordered CIR to grant the refund or tax
credit certificate to Mindanao II.
o It ruled that Mindanao II complied with the twin requisites of

(NAPOCOR). It filed its Quarterly VAT Returns for the second, third, and

It paid input VAT of P7,167,005.84, which were directly

fourth quarters of 2004 on the dates below:

o 2nd Quarter: 26 July 2004
o 3rd Quarter: 22 October 2004
o 4th Quarter: 25 January 2005
(October 6, 2005) Mindanao II filed with BIR its application for the refund
or credit of accumulated unutilized creditable input taxes. It alleged that:
o It was registered with the BIR as a value-added taxpayer
and all its sales are zero-rated under the EPIRA law; and

the EPIRA Law:

It is a generation company; and
It derived sales from power generation
It also ruled that Mindanao II satisfied the requirements for
refund/tax credit under Section 112 of the Tax Code:
There must be zero-rated or effectively zero-rated

sales;
Input taxes must have been incurred or paid;

MONTERO // 3A TAX DIGESTS

The creditable input tax due or paid must be

Issue/s:

attributable to zero-rated sales or effectively zero-

rated sales;
The input VAT payments must not have been

applied against any output liability; and

The claim must be filed within the two-year

WON Mindanao II filed its claim on time by relying on the two-year

prescriptive period for filing an application for refund or credit of

unutilized input VAT

YES
2) WON Mindanao II filed its appeal to the CTA on time by relying on
the two-year period as well
NO

prescriptive period
CIR filed a Motion for Partial Consideration, arguing that the prescriptive
period lapsed on March 5, 2006, or 30 days after, and not two years. They
relied on Section 112(D) of the 1997 Tax Code.
o While this was pending, the SC then promulgated CIR v.
Mirant Pagbilao Corporation (Mirant). Mirant fixed the

Held/Ratio: We deny Mindanao IIs claim for refund or credit of unutilized

input VAT on the ground that its judicial claims were filed out of time, even as
we hold that its application for refund was filed on time.

reckoning date of the two-year prescriptive period for

the application for refund or credit of unutilized input VAT at
the close of the taxable quarter when the relevant sales

YES. The two-year period within which to file a claim is correct.

Mindanao IIs application for refund was filed on time; however, its

judicial claim was filed out of time. This is why the Court ruled that it is

were made, as stated in Section 112(A)

CTA denied CIRs Motion for Partial Consideration and stood by its
reliance to Atlas.
CIR elevated the case to the CTA En Banc and was denied.
o The CTA En Banc said that Mirant cannot be applied to the

not entitled to refund/credit of unutilized input VAT.

The Court emphasized two points:
It is only the administrative claim that must be filed within the
two-year prescriptive period; the judicial claim need not fall

present case because such cannot be applied retroactively

to Mindanao II who relied on Atlas and acted on the faith
o

thereof.
The CTA En Banc also ruled that the 30-day prescriptive

within the two-year prescriptive period; and

The reckoning date of the two-year period is the close of the

Taxable Quarter when the relevant sales were made

So, a taxpayer has two years from the close of the taxable quarter

period that CIR was pushing only applies if CIR actually

when the relevant sales were made to apply for a refund/tax credit to

denied the claim. But in cases of CIR inaction (as in the

the CIR

present case), the 30-day period is not a mandatory

requirement; the judicial claim is seasonably filed as long as
it is filed after the lapse of the 120-day waiting period but
within two years from the date of filing of the return.

2) NO. The 30-Day Period to Appeal is mandatory and jurisdictional.

o So this is the real timeline:

MONTERO // 3A TAX DIGESTS

When a taxpayer files his claim for refund / tax credit, he has

The 30-day period always applies, whether there is a denial

or inaction on the part of the CIR.
As a general rule, the 30-day period to appeal is both
mandatory and jurisdictional.
As an exception to the general rule, premature filing is

up to two years from the close of the taxable quarter when the

relevant sales were made to apply to the CIR.

The CIR, upon such application, has 120 days to resolve the

matter.
If the CIR denies the claim / does not act on it (which is

allowed only if filed between 10 December 2003 and 5

equivalent to denying the claim), the taxpayer has 30 days to

October 2010, when BIR Ruling No. DA-489-03 was still in

appeal to the CTA.

Mindanao II should have filed its appeal to the CTA after 30 days from

force [but now, its not, so it does not apply in the case

the lapse of the 120-day period within which the CTA was supposed to
act on its claim.
o The Court also had its own summary, as follows:
o A. Two-Year Prescriptive Period
It is only the administrative claim that must be filed within the

two-year prescriptive period.

The proper reckoning date for the two-year prescriptive period
is the close of the taxable quarter when the relevant sales

were made.
The only other rule is the Atlas ruling, which applied only from
8 June 2007 to 12 September 2008. Atlas states that the twoyear prescriptive period for filing a claim for tax refund or
credit of unutilized input VAT payments should be counted
from the date of filing of the VAT return and payment of the

tax.
o B. 120+30 Day Period
The taxpayer can file an appeal in one of two ways: (1) file the
judicial claim within thirty days after the Commissioner denies
the claim within the 120-day period, or (2) file the judicial
claim within thirty days from the expiration of the 120-day
period if the Commissioner does not act within the 120-day
period.

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