**Facts:**
Mindanao II Geothermal Partnership, engaged in power generation and sale of electricity, filed Quarterly VAT Returns for the second, third, and fourth quarters of 2004 on specific dates and later amended them on July 12, 2005. On October 6, 2005, it applied for a refund or credit of accumulated unutilized creditable input taxes for these quarters, alleging zero-rated sales under the EPIRA law. The Bureau of Internal Revenue (BIR) did not act on the claim by the February 3, 2006 deadline.
Believing the two-year prescriptive period for filing a judicial claim was to be reckoned from the filing of the VAT Returns, Mindanao II filed a Petition for Review with the Court of Tax Appeals (CTA) on July 21, 2006, fearing the expiration of the prescriptive period. This belief was influenced by the Atlas ruling, which stated the prescriptive period should be counted from the date of filing the VAT return.
The CTA Second Division ruled in favor of Mindanao II, partially granting the refund. The Commissioner of Internal Revenue (CIR) filed a Motion for Partial Reconsideration, arguing the appeal was filed out of time, citing the 30-day period requirement from the BIR’s inaction, as provided by the Tax Code. This contention was later reinforced by the Mirant ruling, which aligned the prescriptive period with the close of the taxable quarter.
The CTA En Banc affirmed the Second Division’s decision, applying the Atlas ruling and rejecting the applicability of the 30-day requirement in cases of inaction by the CIR. However, the Supreme Court (SC) decision in San Roque later clarified the mandatory and jurisdictional nature of the 120+30 day periods, making a distinction from the BIR Ruling No. DA-489-03 period.
**Issues:**
1. Whether the administrative and judicial claims for a VAT refund were filed within the prescribed period.
2. The applicability of the 120+30 day period requirement to the judicial claim’s timely filing.
**Court’s Decision:**
The SC found the administrative claims filed by Mindanao II were timely, given they were within the two-year period from the close of the taxable quarters. However, the judicial claims filed were out of time as they did not observe the 30-day appeal period following the 120-day period provided for the CIR to act on the claim. The SC noted the 30-day appeal period as mandatory and jurisdictional, with San Roque clarifying that this applies irrespective of the BIR’s action or inaction.
**Doctrine:**
1. Only the administrative claim needs to be filed within the two-year prescriptive period; the judicial claim can be filed after provided it is within the 30-day period from either the CIR’s denial or inaction.
2. The proper reckoning date for the two-year prescriptive period for filing a VAT refund claim is the close of the taxable quarter when the relevant sales were made, not the date of the VAT return filing.
**Class Notes:**
– **Prescriptive Period for VAT Refund Claims:** Claims must be administratively filed within two years from the close of the taxable quarter when the sales were made, not from the date of VAT return filing. For judicial claims, a 30-day period to appeal to the CTA applies, commencing from the CIR’s decision or inaction after a 120-day period.
– **Mandatory and Jurisdictional Nature of the 30-day Appeal Period:** The appeal period is non-negotiable and dictates the CTA’s jurisdiction over VAT refund cases. Failure to comply results in the loss of the right to refund or credit.
– **Implications of SC Rulings (Atlas, Mirant, San Roque):** Legal interpretations evolve, and taxpayers must align their actions with the current jurisprudence and statutory provisions. Here, the Court clarified the timeline and procedures for claiming VAT refunds, emphasizing that judicial precedent must be adhered to.
**Historical Background:**
The dispute encapsulates the evolving interpretation of VAT refund claims in the Philippines. Initially, the Atlas doctrine muddled the prescriptive period’s onset, but was later corrected by Mirant and finally clarified by San Roque, which established the precedent applied in this case. This timeline reflects the judiciary’s role in refining tax law interpretations, highlighting the importance of staying abreast with current rulings and legislative amendments for both taxpayers and tax administrators.
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