Centre revamps GST annual returns, clarifies jurisdiction of GSTAT principal bench

The centre has introduced significant changes to the Goods and Services Tax (GST) regime, by revamping the annual GST returns and provided clarity on the jurisdiction on timelines of the principal bench of GST Appellate tribunal. The government has revised the annual GST return (Form GSTR-9), making it more detailed with new tables covering reversals, re-claims, transitional credits, import-related Input Tax Credit (ITC), and auto-populated mismatches. The changes were recommended by the GST council.The Central Board of Indirect taxes and Customs (CBIC) notified the new annual return forms late Wednesday.This shift aims to promote granular compliance, where every credit movement is mapped and reconciled within the return itself. Experts say Taxpayers and professionals will need to undertake deeper reconciliations of GSTR-3B, GSTR-2B, and financial accounts as the changes will be applicable for annual filings of FY 2024-25 onwards."These changes reflect the government's efforts and focus on data-driven compliance and preventive measures to reduce litigation," says Rajat Mohan, Senior Partner, AMRG & Associates.The move, however, significantly raises the responsibility on taxpayers and professionals to undertake deeper reconciliations of GSTR-3B, GSTR-2B, and financial accounts. "By embedding these disclosures upfront, the system aims to save taxpayers from flimsy or avoidable notices, as departmental officers will have a ready-made audit trail in the annual filing," Mohan says.The centre also notified the provisions of Sections 121 to 134 of the Finance Act, 2025, which will be effective October 1, 2025.The provision mandates stricter compliance requirements in return filing and ITC statements, mandatory pre-deposit of 10% of penalty amount for appeals in penalty-only cases, introduction of a Track & Trace mechanism for specified goods with specific penalties for non-compliance.The centre also issued retrospective clarification that certain SEZ warehousing transactions are not treated as “supply”, disallowing refunds of taxes already collected in such cases.Clarity on GSTATAdditionally, the Ministry of Finance has clarified the jurisdiction of the Principal Bench of the GST Appellate Tribunal for hearing certain categories of appeals. Cases involving identical questions of law pending before two or more State Benches or appeals related to specific sections of the Integrated GST Act and CGST Act will be mandatorily heard by the Principal Bench. This move aims to ensure clarity and consistency in the interpretation of important legal issues and interstate tax matters.The centre also notified June 30th as the cut off date for filing appeals before the newly constituted GST Appellate Tribunal in respect of orders communicated prior to 1st April 2026."The Government has allowed ample breathing space for taxpayers awaiting operationalisation of the Tribunal," Rajat Mohan adds."This transitional relaxation will ensure that no litigant is denied the statutory right of appeal merely due to the non-functioning of the forum in the interim," he adds The notification also says that for orders communicated on or after 1st April 2026, appeals must be filed within three months of such communication.