The Supreme Court has clarified that the 120-day and 30-day periods for VAT refund claims are mandatory and jurisdictional, but the Court provided leeway for taxpayers who relied on a previous Bureau of Internal Revenue (BIR) ruling that taxpayers need not wait for the lapse of the 120-day period before seeking judicial relief. This ruling impacts VAT-registered persons seeking refunds for unutilized input tax, specifically those engaged in zero-rated transactions, by specifying the exact timelines to follow when filing refund claims. It also highlights the importance of adhering to the correct procedures to avoid the premature filing of judicial claims, which could lead to their dismissal.

VAT Refund Maze: Can Reliance on Erroneous BIR Advice Save a Premature Claim?

This case revolves around CE Luzon Geothermal Power Company, Inc.’s (CE Luzon) claims for refund of unutilized creditable input Value Added Tax (VAT) for the taxable year 2003. As a VAT-registered entity engaged in the energy industry, CE Luzon incurred input VAT from its operations and sought to claim these as refunds, given its zero-rated sales. The central legal question is whether CE Luzon’s judicial claims were filed within the prescribed period, considering that it filed some of its claims before the expiration of the 120-day period required for the Commissioner of Internal Revenue (CIR) to act on the administrative claim.

The facts show that CE Luzon filed administrative claims for VAT refunds for each quarter of 2003. However, for the first quarter, it filed a judicial claim with the Court of Tax Appeals (CTA) on March 30, 2005, without waiting for the CIR to act on its claim or for the 120-day period to expire. For the second to fourth quarters, CE Luzon filed judicial claims on June 30, 2005, after receiving the CIR’s denial for the second quarter but before the 120-day period expired for the third and fourth quarters. The CIR contested these claims, asserting that CE Luzon failed to comply with the invoicing requirements and that the judicial claims were prematurely filed.

The CTA initially ruled in favor of CE Luzon, but the CTA En Banc reversed this decision, stating that CE Luzon failed to observe the mandatory 120-day period under Section 112(C) of the National Internal Revenue Code (NIRC). The CTA En Banc initially dismissed all claims but later partially granted the claim for the second quarter, relying on the case of Commissioner of Internal Revenue v. Aichi Forging Company of Asia, Inc. Both parties then filed petitions for review, leading to the Supreme Court’s consolidated decision.

The Supreme Court addressed whether the claims were filed within the prescriptive period and if CE Luzon was entitled to the refund for the second quarter of 2003. The Court clarified the interplay between Sections 112(C) and 229 of the NIRC, emphasizing that excess input tax is not an excessively, erroneously, or illegally collected tax. Therefore, Section 112(C), not Section 229, governs claims for refund of creditable input tax.

Section 229 of the NIRC, in relation to Section 204(C), pertains to the recovery of excessively, erroneously, or illegally collected national internal revenue tax. It stipulates that a claim for refund should be made within two years from the date the taxes are paid. This section presupposes that the taxes sought to be refunded were wrongfully paid. The distinction is crucial because it determines which set of rules and timelines apply to the refund claim.

The Court underscored that it is unnecessary to construe and harmonize Sections 112(C) and 229 of the NIRC because creditable input tax is not an excessively, erroneously, or illegally collected tax. When a VAT-registered taxpayer incurs excess input tax, it does not mean that the tax was wrongfully or erroneously paid. Instead, it signifies that the input tax is greater than the output tax, entitling the taxpayer to carry over the excess or seek a refund if it arises from zero-rated transactions. The Court provided that Section 112(C) of the National Internal Revenue Code provides two (2) possible scenarios: the first is when the Commissioner of Internal Revenue denies the administrative claim for refund within 120 days; the second is when the Commissioner of Internal Revenue fails to act within 120 days. Taxpayers must await either for the decision of the Commissioner of Internal Revenue or for the lapse of 120 days before filing their judicial claims with the Court of Tax Appeals. Failure to observe the 120-day period renders the judicial claim premature.

The Supreme Court found that CE Luzon’s reliance on Atlas Consolidated Mining and Development Corporation v. Commissioner of Internal Revenue was misplaced. Atlas did not squarely address the issue regarding the prescriptive period in filing judicial claims for refund of creditable input tax. It was the Aichi case that directly tackled and interpreted Section 112(C) of the NIRC. The Court reiterated the Aichi doctrine in San Roque, holding that the 120-day and 30-day periods in Section 112(C) of the NIRC are both mandatory and jurisdictional.

In this light, the Court found that only CE Luzon’s second quarter claim was filed on time, while its claims for refund of creditable input tax for the first, third, and fourth quarters of taxable year 2003 were filed prematurely. It did not wait for the Commissioner of Internal Revenue to render a decision or for the 120-day period to lapse before elevating its judicial claim with the Court of Tax Appeals.

However, the Supreme Court recognized an exception based on CE Luzon’s reliance on Bureau of Internal Revenue (BIR) Ruling DA-489-03, which stated that a taxpayer-claimant need not wait for the lapse of the 120-day period before seeking judicial relief with the CTA. The Court acknowledged that this ruling, though an erroneous interpretation of the law, had misled taxpayers into prematurely filing judicial claims. Therefore, the Court shielded CE Luzon from the vice of prematurity for relying on this BIR ruling, which was in effect from December 10, 2003, until its reversal on October 6, 2010, in Aichi.

Building on this principle, the Court emphasized that taxpayers should not be prejudiced by an erroneous interpretation by the Commissioner, especially on a difficult question of law. Thus, CE Luzon could claim the benefit of BIR Ruling DA-489-03, and its judicial claims for refund of creditable input tax for all quarters of 2003 were considered timely filed.

Considering that CE Luzon’s judicial claims for the first, third, and fourth quarters of 2003 should be considered as timely filed, the case was remanded to the Court of Tax Appeals for the proper computation of creditable input tax to which CE Luzon is entitled. Regarding the Commissioner of Internal Revenue’s contestation of CE Luzon’s compliance with documentation requirements, the Court reiterated that only questions of law may be raised in a Rule 45 Petition. The determination of whether CE Luzon duly substantiated its claim for refund of creditable input tax for the second quarter of taxable year 2003 is a factual matter that is generally beyond the scope of a Petition for Review on Certiorari.

FAQs

What was the key issue in this case?	The key issue was whether CE Luzon’s judicial claims for VAT refunds were filed within the prescriptive period, especially considering that some claims were filed before the 120-day period for the CIR to act on the administrative claim had expired.
What is the 120-day rule under Section 112(C) of the NIRC?	Section 112(C) of the NIRC requires taxpayers to wait 120 days from the submission of complete documents for the CIR to decide on their administrative claim for a VAT refund. The judicial claim can be filed only after the CIR’s decision or after the 120-day period has lapsed.
Why did CE Luzon file judicial claims before the 120-day period expired?	CE Luzon relied on BIR Ruling DA-489-03, which stated that taxpayers need not wait for the 120-day period before seeking judicial relief.
How did the Supreme Court address the premature filing of judicial claims?	The Supreme Court recognized that the BIR ruling had misled taxpayers and, therefore, shielded CE Luzon from the consequences of prematurely filing its judicial claims, considering it filed its claims before the Aichi ruling.
What is the difference between Section 112(C) and Section 229 of the NIRC?	Section 112(C) governs claims for refund of creditable input tax, while Section 229 pertains to the recovery of excessively, erroneously, or illegally collected national internal revenue tax.
What was the significance of the Aichi case in this decision?	The Aichi case clarified that the 120-day and 30-day periods in Section 112(C) of the NIRC are mandatory and jurisdictional, reversing the interpretation that taxpayers could file judicial claims before the 120-day period expired.
What did the Supreme Court ultimately decide in this case?	The Supreme Court granted CE Luzon’s petition, ruling that its judicial claims were timely filed due to its reliance on the BIR ruling. The case was remanded to the CTA for the proper computation of creditable input tax.
What is the practical implication of this ruling for VAT-registered taxpayers?	VAT-registered taxpayers must generally adhere to the mandatory 120-day period before filing judicial claims for VAT refunds, however, taxpayers who filed their claims during the applicability of the BIR ruling may still be protected.

In conclusion, the Supreme Court’s decision provides clarity on the mandatory nature of the 120-day rule for VAT refund claims. While it upheld the general principle, it also demonstrated a willingness to provide relief to taxpayers who relied on previous, albeit erroneous, BIR rulings. This ruling reinforces the need for taxpayers to stay informed of changes in tax regulations and to comply with the prescribed procedures to ensure the validity of their claims.

For inquiries regarding the application of this ruling to specific circumstances, please contact ASG Law through contact or via email at frontdesk@asglawpartners.com.

Disclaimer: This analysis is provided for informational purposes only and does not constitute legal advice. For specific legal guidance tailored to your situation, please consult with a qualified attorney.
Source: CE Luzon Geothermal Power Company, Inc. vs. Commissioner of Internal Revenue, G.R. No. 199676-77, July 26, 2017