VALUE ADDED TAX (VAT) CASES

G.R. No. 203774, March 11, 2015

CARGILL PHILIPPINES, INC., Petitioner, v. COMMISSIONER OF INTERNAL REVENUE, Respondent.
Facts: Cargill is a domestic corporation duly organized and existing under Philippine laws whose
primary purpose is to own, operate, run, and manage plants and facilities for the production,
crushing, extracting, or otherwise manufacturing and refining of coconut oil, coconut meal, vegetable
oil, lard, margarine, edible oil, and other articles of similar nature and their by-products. It is a VATregistered entity with Tax Identification No./VAT Registration No.000-110-659-000. As such, it filed
its quarterly VAT returns for the second quarter of calendar year 2001 up to the third quarter of fiscal
year 2003, covering the period April 1, 2001 to February 28, 2003, which showed an overpayment of
P44,920,350.92 and, later, its quarterly VAT returns for the fourth quarter of fiscal year 2003 to the
first quarter of fiscal year 2005, covering the period March 1, 2003 to August 31, 2004 which
reflected an overpayment of P31,915,642.26.6 Cargill maintained that said overpayments were due
to its export sales of coconut oil, the proceeds of which were paid for in acceptable foreign currency
and accounted for in accordance with the rules and regulations of the Bangko Sentralng Pilipinas and,
thus, are zero-rated for VAT purposes.
On June 27, 2003, Cargill filed an administrative claim for refund of its unutilized input VAT in the
amount of P26,122,965.81 for the period of April 1, 2001 to February 28, 2003 (first refund claim)
before the Bureau of Internal Revenue (BIR). Thereafter, or on June 30, 2003, it filed a judicial claim
for refund, by way of a petition for review, before the CTA, docketed as CTA Case No. 6714. On
September 29, 2003, it subsequently filed a supplemental application with the BIR increasing its
claim for refund of unutilized input VAT to the amount of P27,847,897.72.
On May 31, 2005, Cargill filed a second administrative claim for refund of its unutilized input VAT in
the amount of P22,194,446.67 for the period of March 1, 2003 to August 31, 2004 (second refund
claim) before the BIR. On even date, it filed a petition for review before the CTA, docketed as CTA
Case No. 7262.
For its part, respondent Commissioner of Internal Revenue (CIR) claimed, inter alia, that the
amounts being claimed by Cargill as unutilized input VAT in its first and second refund claims were
not properly documented and, hence, should be denied.
CTA:
In an Amended Decision22dated April 20, 2011, the CTA Division preliminarily denied the individual
motions of both parties, to wit: (a) CIRs motion for reconsideration for lack of notice of hearing; (b)
CIRs motion to dismiss on the ground of estoppel; and (c) Cargills motion for reconsideration for
lack of merit.
Separately, however, the CTA Division superseded and consequently reversed its August 24, 2010
Decision. Citing the case of CIR v. Aichi Forging Company of Asia, Inc. (Aichi),24it held that the 120day period provided under Section 112(D) of the National Internal Revenue Code (NIRC) must be
observed prior to the filing of a judicial claim for tax refund.25As Cargill failed to comply therewith,
the CTA Division, without ruling on the merits, dismissed the consolidated cases for being
prematurely filed
CTA EN BANC:
In a Decision27 dated June 18, 2012, the CTA En Banc affirmed the CTA Divisions April 20, 2011
Amended Decision, reiterating that Cargills premature filing of its claims divested the CTA of
jurisdiction, and perforce, warranted the dismissal of its petitions.
Issue: WON the CTA En Banc correctly affirmed the CTA Divisions outright dismissal of Cargills
claims for refund of unutilized input VAT on the ground of prematurity.

Held: WHEREFORE, the petition is PARTLY GRANTED.

The

petition

is

partly

meritorious.

Allowing the refund or credit of unutilized input VAT finds its genesis in Executive Order No.
273,31series of 1987, which is recognized as the Original VAT Law. Thereafter, it was amended
through the passage of Republic Act No. (RA) 7716,32 RA 8424,33 and, finally by RA 9337,34 which
took effect on November 1, 2005. Considering that Cargills claims for refund covered periods before
the effectivity of RA 9337, Section 112 of the NIRC, as amended by RA 8424, should, therefore, be
the
governing
law,35the
pertinent
portions
of
which
read:
Section 112. Refunds or Tax Credits of Input Tax.
(A) Zero-rated or Effectively Zero-rated Sales. any VAT-registered person, whose sales are zerorated 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: x x x.chanrobleslaw
xxxx
(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 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. (Emphases and underscoring supplied)
xxxx
In the landmark case of Aichi, it was held that the observance of the 120-day period is a mandatory
and jurisdictional requisite to the filing of a judicial claim for refund before the CTA. As such, its nonobservance would warrant the dismissal of the judicial claim for lack of jurisdiction. It was, withal,
delineated in Aichi that the two (2)-year prescriptive period would only apply to administrative
claims, and not to judicial claims.36 Accordingly, once the administrative claim is filed within the two
(2)-year prescriptive period, the taxpayer-claimant must wait for the lapse of the 120-day period
and, thereafter, he has a 30-day period within which to file his judicial claim before the CTA, even if
said 120-day and 30-day periods would exceed the aforementioned two (2)-year prescriptive period.
Nevertheless, the Court, in the case of CIR v. San Roque Power Corporation38 (San Roque),
recognized an exception to the mandatory and jurisdictional nature of the 120-day period. San
Roqueenunciated that BIR Ruling No. DA-489-03 dated December 10, 2003, which expressly declared
that the 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, provided a valid claim for equitable estoppel
under
Section
24639 of
the
NIRC.
In the more recent case of Taganito Mining Corporation v. CIR,41 the Court reconciled the
pronouncements in Aichi and San Roque, holding that from December 10, 2003 to October 6,
2010which refers to the interregnum when BIR Ruling No. DA-489-03 was issued until the date of

promulgation of Aichi, taxpayer-claimants need not observe the stringent 120-day period; but before
and aftersaid window period, the mandatory and jurisdictional nature of the 120-day period remained
in
force, viz.:
Reconciling the pronouncements in the Aichi and San Roque cases, the rule must therefore be
that during the period December 10, 2003 (when BIR Ruling No. DA-489-03 was issued) to
October 6, 2010 (when the Aichi case was promulgated),taxpayers-claimants need not observe
the 120-day period before it could file a judicial claim for refund of excess input VAT before the
CTA. Before and after the aforementioned period ( i.e., December 10, 2003 to October 6,
2010), the observance of the 120-day period is mandatory and jurisdictional to the filing of
such claim.42 (Emphases and underscoring supplied)
In this case, records disclose that anent Cargills first refund claim, it filed its administrative claim
with the BIR on June 27, 2003, and its judicial claim before the CTA on June 30, 2003, or before the
period when BIR Ruling No. DA-489-03 was in effect, i.e., from December 10, 2003 to October
6, 2010. As such, it was incumbent upon Cargill to wait for the lapse of the 120-day period before
seeking relief with the CTA, and considering that its judicial claim was filed only after three (3) days
later, the CTA En Banc, thus, correctly dismissed Cargills petition in CTA Case No. 6714for being
prematurely
filed.
In contrast, records show that with respect to Cargills second refund claim, its administrative and
judicial claims were both filed on May 31, 2005, or during the period of effectivity of BIR Ruling
NO. DA-489-03, and, thus, fell within the exemption window period contemplated in San Roque,
i.e., when taxpayer-claimants need not wait for the expiration of the 120-day period before seeking
judicial relief. Verily, the CTA En Banc erred when it outrightly dismissed CTA Case No. 7262on the
ground
of
prematurity.
This notwithstanding, the Court finds that Cargills second refund claim in the amount of
P22,194,446.67 which allegedly represented unutilized input VAT covering the period March 1, 2003
to August 31, 2004 should not be instantly granted. This is because the determination of Cargills
entitlement to such claim, if any, would necessarily involve factual issues and, thus, are evidentiary in
nature which are beyond the pale of judicial review under a Rule 45 petition where only pure
questions of law, not of fact, may be resolved. 43 Accordingly, the prudent course of action is to
remand CTA Case No. 7262 to the CTA Division for resolution on the merits, consistent with the
Courts ruling in Panay Power Corporation v. CIR.
G.R. No. 185666, February 04, 2015
NIPPON EXPRESS (PHILIPPINES)
REVENUE,Respondents.

CORP., Petitioner, v. COMMISSIONER

OF

INTERNAL

Facts: Petitioner is a corporation duly organized and existing under the laws of the Republic of the
Philippines, registered with the Securities and Exchange Commission (SEC) under Certificate of
Registration No. ASO95-005669, and with principal office at U-2701 Yuchengco Tower, RCBC Plaza,
6819 Ayala Ave., Salcedo Village, Makati City.
Likewise, petitioner is registered with the Large Taxpayers District Office of the Bureau of Internal
Revenue in Makati City as, among others, a Value-Added Tax (VAT) taxpayer rendering freight
forwarding services.
Respondent, on the other hand, is the duly appointed Commissioner of Internal Revenue vested with
power to decide, approve, and grant refunds or tax credits of overpaid internal revenue taxes as
provided by law and holds office and may be served with summons, orders, pleadings, and other
processes at BIR Revenue Region 8, 5/F Atrium Bldg., Makati Ave., Makati City.
The precedent facts, as culled from the records are as follows:

For the calendar year 2000, petitioners gross receipts were primarily derived from rendering its
services to Philippine Economic Zone Authority (PEZA)-registered clients. Likewise, it incurred total
sales of P1,063,357,608.74, which as shown in petitioners Amended Quarterly VAT Return:

Also, for the same year, petitioner paid input taxes amounting to P31,846,253.57 and apportioning
this amount with its total sales above in accordance with Section 112 of the 1997 Tax Code, as
amended; the amount of total sales attributable to zero-rated sales would be P24,826,667.61.
Under the premise that it is entitled to a refund of the amount of P24,826,667.61, petitioner filed
four separate applications for tax credit/refund with the One-Stop Shop Inter-Agency Tax Credit and
Duty Drawback Center of the Department of Finance (OSSAC-DOF) on September 24, 2001.
Receiving no resolution from OSSAC-DOF, petitioner filed the instant petition for review on April 24,
2002 pursuant to Section 112 in relation to Section 229 of the 1997 Tax Code, as amended.
CTA: In a Decision dated 15 June 2007,7 the CTA in Division denied due course and accordingly
dismissed petitioners claim for the issuance of a TCC on the ground of its failure to comply with the
substantiation requirements.
CTA EN BANC: The CTA En Banc agreed with the court a quos findings that the evidence submitted
by petitioner, i.e. sales invoices, transfer slips, credit memos, cargo manifests, and credit notes, as
well as formal report of the independent certified public accountant (ICPA), to prove its zero-rated
sales, were insufficient so as to entitle it to the issuance of a TCC since the aforesaid legal provisions

do not provide for any other document that can be used as an alternative to, or in lieu of an invoice
and official receipts.
Issue: WON petitioner is entitled to a TCC in the amount of P24,826,667.61 allegedly representing
its excess and unutilized input VAT for the taxable year 2000, in accordance with the provisions of the
NIRC of 1997, as amended, other pertinent laws, and applicable jurisprudential proclamations.
Held: WHEREFORE, the claim for refund is by prescription BARRED.
At the outset, in a petition for review on certiorari under Rule 45 of the Rules of Court, only questions
of law may be raised.15 The Court is not a trier of facts and does not normally undertake the reexamination of the evidence presented by the contending parties during the trial of the case
considering that the findings of facts of the (CTA) are conclusive and binding on the Court 16 and
they carry even more weight when the (CTA En Banc) affirms the factual findings of the trial court. 17
However, this Court had recognized several exceptions to this rule,18 including instances when the
appellate court manifestly overlooked relevant facts not disputed by the parties, which, if properly
considered, would probably justify a different conclusion.
In Commissioner of Internal Revenue v. San Roque Power Corporation, Taganito Mining Corporation
v. Commissioner of Internal Revenue, and Philex Mining Corporation v. Commissioner of Internal
Revenue (San Roque case),19 this Court has finally settled the issue on proper observance of the
prescriptive periods in claiming for refund of creditable input tax due or paid attributable to any zerorated or effectively zero-rates sales. In view of the foregoing jurisprudential pronouncements, there
appears to be an imperious need for this Court to review the factual findings of the CTA in order to
attain a complete determination of the issue presented.
Records reveal that the CTA in Division in C.T.A. Case No. 6464 merely focused on the compliance
with the substantiation requirements, which particularly ruled that the evidence submitted by
petitioner to prove its zero-rated sales were insufficient so as to entitle it to the issuance of a TCC.
The same findings were adopted and affirmed in toto by the CTA En Banc in the assailed 20 August
2008 Decision.20
chanroblesvirtuallawlibrary

While it is true that the substantiation requirements in establishing a refund claim is a valid issue, the
Court finds it imperative to first and foremost determine whether or not the CTA properly acquired
jurisdiction over petitioners claim covering taxable year 2000, taking into consideration the
timeliness of the filing of its judicial claim pursuant to Section 112 of the NIRC of 1997, as amended,
and consistent with the pronouncements made in the San Roque case. Clearly, the claim of
petitioner for the TCC can proceed only upon compliance with the aforesaid jurisdictional
requirement.
Relevant to the foregoing, Section 7 of R.A. No. 1125, 21 which was thereafter amended by R.A. No.
9282,22clearly defined the appellate jurisdiction of the CTA, to wit:
chanRoble svirtualLawlibrary

Section 7. Jurisdiction. - The Court of Tax Appeals shall exercise exclusive appellate jurisdiction to
review by appeal, as herein provided.
(1) Decisions of the Commissioner of Internal Revenue in cases involving disputed
assessments, refunds of internal revenue taxes, fees or other charges, penalties imposed in
relation thereto, or other matters arising under the National Internal Revenue Code or other law or
part
of
law
administered
by
the
Bureau
of
Internal
Revenue;

chanrobleslaw

x x x.23 (Emphasis supplied)

Moreover, Section 11 of the same law prescribes how the said appeal should be taken. It reads:

chanRoblesvirtualLa wlibrary

Section 11. Who may appeal; effect of appeal. Any person, association or corporation
adversely affected by a decision or ruling of the Collector of Internal Revenue, the Collector of
Customs or any provincial or city Board of Assessment Appeals may file an appeal in the Court of
Tax Appeals within thirty days after the receipt of such decision or ruling. 24x x x (Emphasis
and underscoring supplied)
The timeliness in the administrative and judicial claims can be found in Section 112 of the NIRC of
1997, as amended, which reads:
chanRoble svirtualLawlibrary

SEC.

112. Refunds

or

Tax

Credits

of

Input

Tax.

(A) Zero-rated or Effectively Zero-rated Sales. Any VAT-registered person, whose sales are zerorated 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:
x
x
x.
x

(D)25Period 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)
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
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.
x x x x. (Emphasis and underscoring supplied)
As mentioned earlier, the proper interpretation of the afore-quoted provision was finally settled in
the San Roque case26 by this Court sitting En Banc. The relevant portions of the discussion pertinent
to the focal issue in the present case are quoted hereunder as follows:
chanRoblesvirtualLa wlibrary

To repeat, a claim for tax refund or credit, like a claim for tax refund exemption, is construed strictly
against the taxpayer. One of the conditions for a judicial claim of refund or credit under the VAT
System is compliance with the 120+30 day mandatory and jurisdictional periods. Thus,
strict compliance with the 120+30 day periods is necessary for such a claim to prosper,
whether before, during, or after the effectivity of the Atlas doctrine, except for the period
from the issuance of BIR Ruling No. DA-489-03 on 10 December 2003 to 6 October 2010
when the Aichi doctrine was adopted, which again reinstated the 120+30 day periods as
mandatory and jurisdictional.27 (Emphasis supplied)
The same disposition was declared in Mindanao II Geothermal Partnership v. Commissioner of
Internal Revenue, and Mindanao I Geothermal Partnership v. Commissioner of Internal
Revenue,28 which, for emphasis, further provided a Summary of Rules on Prescriptive Periods
Involving VAT as a guide for all parties concerned, to wit:
chanRoble svirtualLawlibrary

We summarize the rules on the determination of the prescriptive period for filing a tax refund
or credit of unutilized input VAT as provided in Section 112 of the 1997 Tax Code, as

follows:

chanRoble svirtualLawlibrary

(1) An administrative claim must be filed with the CIR within two years after the close of the taxable
quarter
when
the
zero-rated
or
effectively
zero-rated
sales
were
made.
(2) The CIR has 120 days from the date of submission of complete documents in support of the
administrative claim within which to decide whether to grant a refund or issue a tax credit
certificate. The 120-day period may extend beyond the two-year period from the filing of the
administrative claim if the claim is filed in the later part of the two-year period. If the 120-day
period expires without any decision from the CIR, then the administrative claim may be
considered
to
be
denied
by
inaction.
(3) A judicial claim must be filed with the CTA within 30 days from the receipt of the CIRs
decision denying the administrative claim or from the expiration of the 120-day period
without
any
action
from
the
CIR.
(4) All taxpayers, however, 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 October 6, 2010,
as an exception to the mandatory and jurisdictional 120+30 day periods. 29(Emphasis
supplied)
Certainly, it is evident from the foregoing jurisprudential pronouncements that a taxpayer-claimant
only had a limited period of thirty (30) days from the expiration of the one hundred twenty (120)-day
period of inaction of the Commissioner of Internal Revenue (CIR) to file its judicial claim with the
CTA, with the exception of claims made during the effectivity of Bureau of Internal Revenue (BIR)
Ruling No. DA-489-03 (from 10 December 2003 to 5 October 2010). 30 Failure to do so, the judicial
claim
shall
prescribe
or
be
considered
as
filed
out
of
time.
Applying the foregoing discussion to the present case, although it appears that petitioner has indeed
complied with the required two-year period within which to file a refund/tax credit claim with the BIR
(OSSAC-DOF in this case) by filing all its administrative claims on 24 September 2001 (within the
period from the close of the taxable quarters for the year 2000, when the sales were made), this
Court finds that petitioners corresponding judicial claim was filed beyond the 30-day period, detailed
hereunder as follows:

Section 112(D) of the NIRC of 1997 categorically states that in case of failure on the part of the
respondent to act on the application within the 120-day period prescribed by law, petitioner only has
30 days after the expiration of the 120-day period to appeal the unacted claim with the CTA. Since
petitioners judicial claim for the aforementioned quarters for taxable year 2000 was filed before the
CTA only on 24 April 2002,32 which was way beyond the mandatory 120+30 days to seek judicial
recourse, such non-compliance with the mandatory period of 30 days is fatal to its refund claim on

the ground of prescription. Consequently, the CTA had no jurisdiction over the instant claim of
petitioner as the petition was belatedly filed.
It must be emphasized that jurisdiction over the subject matter or nature of an action is fundamental
for a court to act on a given controversy,33 and is conferred only by law and not by the consent or
waiver upon a court which, otherwise, would have no jurisdiction over the subject matter or nature of
an action. Lack of jurisdiction of the court over an action or the subject matter of an action cannot
be cured by the silence, acquiescence, or even by express consent of the parties.34 If the court has
no jurisdiction over the nature of an action, its only jurisdiction is to dismiss the case. The court
could not decide the case on the merits.
The CTA, even if vested with special jurisdiction, is, as courts of general jurisdiction can only take
cognizance of such matters as are clearly within its statutory authority.36 Relative thereto, when it
appears from the pleadings or the evidence on record that the court has no jurisdiction over the
subject matter, the court shall dismiss the claim.
Finally for academic discussion, as regards the substantiation requirements, it is worthy to mention
that in Kepco Philippines Corporation v. Commissioner of Internal Revenue,38 the High Court ruled
that under the law, a VAT invoice is necessary for every sale, barter or exchange of goods or
properties while a VAT official receipt properly pertains to every lease of goods or properties, and
every sale, barter or exchange of services. In other words, the VAT invoice is the sellers best proof
of the sale of the goods or services to the buyer while the VAT receipt is the buyers best evidence of
the payment of goods or services received from the seller. Thus, the High Court concluded that VAT
invoice and VAT receipt should not be confused as referring to one and the same thing. Certainly,
neither does the law intend the two to be used interchangeably.
All told, the CTA has no jurisdiction over petitioners judicial appeal considering that its Petition for
Review was filed beyond the mandatory 30-day period pursuant to Section 112(D)39 of the NIRC of
1997, as amended, and consistent with the ruling in the San Roque case. Consequently, petitioners
instant claim for refund must be denied.