The Ministry of Finance, Department of Revenue, has issued Notification introducing significant amendments to the Central Goods and Services Tax (CGST) Rules, 2017 which includes faster refunds, GSTAT single-member benches and new annual return formats.
Acting on the recommendations of the GST Council, the Central Government has exercised its powers under Section 164 of the CGST Act, 2017 to notify the Central Goods and Services Tax (Third Amendment) Rules, 2025, which will come into effect from 22 September 2025, unless specified otherwise.
One of the important changes is the revision in Rule 31A(2), where the figures have been updated from “128” to “140,” streamlining valuation procedures in line with GST reforms. Similarly, Rule 39(1A), effective from 1 April 2025, has been amended to expand the scope of input tax credit (ITC) under both the CGST Act and the IGST Act.
Refund provisions have also been strengthened. With effect from 1 October 2025, Rule 91 has been revised to mandate that refund rejection orders must be issued within seven days of acknowledgment in Form GST RFD-04. This system-driven, risk-based approach is expected to speed up refund processing and reduce delays.
Major changes have been introduced in the appeal procedures under Rules 110 and 111. New acknowledgment formats, such as Form GST APL-02A and APL-02B, have been prescribed for appeals before the GST Appellate Tribunal. Importantly, the amendments also allow single-member benches to hear appeals that do not involve substantial questions of law, which will help in quicker disposal of cases. Clearer guidelines on jurisdictional limits and transfers of appeals have also been included.
Further, Rule 113 has been amended to require the Tribunal to issue a summary of its orders in Form GST APL-04A. This will ensure that the final amount of demand upheld is clearly recorded and communicated, enhancing transparency in dispute resolution.
Annual return filing has undergone significant changes as well. Structural modifications have been introduced in Form GSTR-9 to provide a more accurate reflection of ITC reversals and re-availments under Rules 37, 37A, 38, 42, and 43. The revised format will also allow reporting of imported ITC utilized in subsequent financial years and adjustments made through credit or debit notes filed up to 30 November of the following year. Similarly, in Form GSTR-9C (Reconciliation Statement), new disclosures have been mandated for supplies covered under Section 9(5) of the CGST Act, which makes e-commerce operators liable for tax.
In addition to these changes, new forms have been introduced. Form GST APL-02A provides acknowledgment for appeal filing, while Form GST APL-04A summarizes Tribunal orders. The format of Form GST APL-05, which is used to file appeals before the Appellate Tribunal, has also been revised to align with the new procedures.
Notification Details
Notification No. 13/2025–Central Tax
Date: 17/09/2025
