Facts of the Case:

In this case, the petitioner challenged refund sanction/rejection Order dated 03.10.2024 passed in Form GST RFD-06 for the tax period July 2022, by which the refund claim was rejected as time-barred under Section 54(3) of the CGST Act, 2017.

The petitioner had initially filed a refund application on 04.07.2024, which was within two years from the relevant date i.e. 26.07.2022, as prescribed under Section 54(3). A deficiency memo dated 18.07.2024 was issued by the department, pursuant to which the petitioner filed a fresh refund application on 14.08.2024.

The respondents rejected the refund on the ground that the application dated 14.08.2024 was filed beyond the limitation period. The appeal filed by the petitioner was also dismissed by the appellate authority, leading to the present writ petition. Reliance placed upon the decision of the same High Court in M/s. Amidc Automation Technologies Pvt. Ltd. v. CBIC, wherein it was held that limitation for refund must be reckoned from the date of the original application and not from subsequent applications filed pursuant to deficiency memos.

Issue: Whether a refund application originally filed within the limitation period under Section 54(3) of the CGST Act can be rejected as time-barred by reckoning limitation from a subsequent application filed pursuant to a deficiency memo?

Held that:

The Court held that since the petitioner had initially filed the refund application on 04.07.2024, which was well within the prescribed limitation period, that date alone must be considered for computing limitation under Section 54(3). Filing a revised refund application pursuant to a deficiency memo does not amount to a fresh claim for the purpose of limitation. Treating the subsequent application as the basis for limitation was held to be clearly erroneous.

The Court followed its earlier ruling in M/s. Amidc Automation Technologies Pvt. Ltd., wherein it was categorically held that refund claims filed within limitation cannot be rejected merely because of repeated or revised applications, especially when delay occurred due to procedural deficiencies pointed out by the department.

The findings recorded by the refund authority and the appellate authority rejecting the refund as time-barred were held to be contrary to law and unsustainable.

Case Name: Homag India Private Limited, Represented By Its Managing Director Sri. Aravind N.S. Versus The Joint Commissioner of Central Tax And The Assistant Commissioner of Central Tax dated 12.12.2025

To read the complete judgement 2025 Taxo.online 3511