The Ministry of Finance has issued Notification No. 13/2025 - Central Tax, introducing the Central Goods and Services Tax (Third Amendment) Rules, 2025. The amendments, effective from September 22, 2025, bring significant changes to GST compliance, particularly in refund processing, appellate procedures, and annual return reporting.
Key Highlights of the Third Amendment Rules, 2025
Refund Procedure Simplified
- Rule 91 has been substituted to mandate that refund orders (Form GST RFD-04) must be issued within 7 days of acknowledgment, based on system-driven risk assessment.
- If refund is withheld, reasons must be recorded in writing and the process shifted to Rule 92.
Appeals Before GSTAT
- New Rule 110A introduces procedure for appeals before a single-member bench of the GST Appellate Tribunal (GSTAT).
- If a question of law is involved, the appeal will be transferred back to a division bench.
- Fresh formats such as Form GST APL-02A and Form GST APL-04A have been introduced to streamline appeal registration and orders.
Annual Return (GSTR-9) Changes
- Extensive modifications made in Form GSTR-9 and GSTR-9C, including reporting of Input Tax Credit (ITC) adjustments, reversals, and carry-forwards across FYs 2023-24, 2024-25, and onwards.
- Separate disclosure for ITC reversed under Rules 37, 37A, 38, 42, and 43.
- Auto-population features added for certain ITC tables to minimize manual errors.
Impact on E-Commerce Operators
- Amendments specifically require reporting of supplies covered under Section 9(5) of CGST Act (where e-commerce operators are liable to pay tax).
- New rows in GSTR-9 and GSTR-9C ensure proper disclosure of such transactions.
Expert Take
Tax professionals believe these amendments will speed up refund disbursals, bring greater clarity in appellate processes and ensure accurate ITC reconciliation. However, businesses will need to adapt quickly to the revised formats to avoid compliance lapses.
Conclusion
With these amendments, the government aims to strengthen GST compliance through automation, transparency, and quicker dispute resolution. Businesses and tax practitioners are advised to carefully review the updated rules and revise their GST return filing and appeal strategies before the new provisions take effect.
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