Manual GST refund filing may be processed where Rule 97A treats electronic filing references as including manual applications.

Rule 97A of the CGST Rules expressly deems references to electronic filing on the common portal to include manual filing of the relevant refund application or procedure, so a manual refund claim cannot be rejected merely for lack of electronic filing. That statutory rule operates within the refund scheme under Chapter X and prevails over administrative instructions or circulars, which cannot override it. Rule 89 must be applied consistently with Rule 97A, and technical difficulties should not defeat legitimate refund claims. The appellate order rejecting the refund was therefore liable to be set aside and the manual application processed.

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Issues: Whether a manual refund application could be processed notwithstanding the electronic filing requirement, and whether the appellate order rejecting such refund claim deserved to be quashed.

Analysis: Rule 97A of the Central Goods and Services Tax Rules, 2017 contains a non-obstante clause and expressly provides that any reference to electronic filing on the common portal shall include manual filing of the relevant application or procedure. This statutory rule operates within Chapter X governing refunds and cannot be overridden or diluted by administrative instructions or circulars issued under the Act. Rule 89 prescribes the refund mechanism, but it must be read consistently with Rule 97A, which preserves manual filing where the process so requires. The Court also emphasised that technical difficulties should not defeat legitimate refund claims and that the system ought to be administered in a more assessee-friendly manner.

Conclusion: The manual refund application was required to be processed, and the impugned appellate order was liable to be set aside in favour of the assessee.

Ratio Decidendi: Where a statutory rule expressly permits manual filing notwithstanding electronic filing requirements, administrative circulars cannot override or control that rule.

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