GST Third Amendment Rules 2025 | Key Changes Notified by CBIC

Notification No. 13/2025-Central Tax, Dated 17-09-2025

1. Introduction

The Central Board of Indirect Taxes and Customs (CBIC) has issued a notification amending the CGST Rules, 2017. These amendments introduce several procedural and compliance-related changes, particularly concerning refund processing, appellate procedures, and reporting in annual GST returns. The changes are aimed at improving efficiency, transparency, and risk management in GST administration.

2. Amendments to Refund Procedures

A key amendment relates to the issuance of refund orders in FORM GST RFD-04. Under the revised rules, such orders will now be issued within seven days, based on a system-driven risk evaluation mechanism. This measure is expected to expedite refund disbursals while maintaining strong checks against fraud. At the same time, authorities retain the discretion to proceed directly under Rule 92, allowing for detailed examination in appropriate cases.

3. Changes in Appellate Procedures

The notification also introduces significant reforms in appellate procedures. Appeals that do not involve questions of law can now be heard by a single Member Bench, easing the burden on appellate forums and facilitating faster disposal of cases. Additionally, several new and revised forms have been introduced, including FORM GST APL-02A and FORM GST APL-04A, along with the substitution of FORM GST APL-05, APL-06, and APL-07, marking a comprehensive revamp of the appellate framework.

4. Revisions in Annual GST Returns

Substantial modifications have also been made in FORM GSTR-9 and FORM GSTR-9C. These include changes to the disclosure of input tax credit, cross-year availment, reclaimed credit, and reconciliation of tax liabilities. Taxpayers will also be required to report supplies on which tax is payable by e-commerce operators, bringing greater accuracy and alignment with evolving GST provisions. The amendments will take effect from 22nd September 2025, with certain provisions effective from 1st April 2025 and 1st October 2025.

5. Restriction on Provisional Refunds

In addition, through Notification No. 14/2025 – Central Tax, CBIC has specified that from 1st October 2025, provisional refunds shall not be admissible in cases where Aadhaar authentication has not been completed. Refunds will also be disallowed for applicants engaged in the supply of specified goods such as areca nuts, pan masala, tobacco and its substitutes, and essential oils. These measures aim to tighten controls on high-risk sectors and prevent misuse of refund provisions.

6. Conclusion

The amendments to the CGST Rules, 2017, mark a significant step in strengthening GST compliance and governance. By combining faster refunds with stricter risk controls, streamlining appellate processes, revising return formats, and tightening refund eligibility, the CBIC has sought to balance ease of doing business with robust revenue protection.

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