GST annual return for FY 2025-26: what changed in the reconciliation
The revised GSTR-9C tables and the three reconciliation items that most commonly cause a mismatch notice.
The revised GSTR-9C tables and the three reconciliation items that most commonly cause a mismatch notice. This note is one of a series of factual compliance notes published by Lalit Mohan Tyagi & Co.; it is general information, not advice for a specific person or entity. Read the full note below, or see the compliance calendar for the underlying due dates.
The annual return in Form GSTR-9 and the reconciliation statement in Form GSTR-9C are due by 31 December 2026 for the financial year ended 31 March 2026. Registered persons with an aggregate turnover above the prescribed threshold must file both.
Three reconciliation items account for most of the mismatch notices we see. The first is turnover reported in the audited financial statements against turnover declared in the returns, where the difference usually arises from unbilled revenue, credit notes issued after the year end, and supplies recorded net of discount in the books but gross in the return.
The second is input tax credit availed in the returns against credit recorded in the books. Credit reversed under rule 42 and rule 43, credit availed in a later period, and credit on invoices where the supplier has not filed, all need to be tracked as reconciling items rather than absorbed silently.
The third is tax paid under reverse charge. Where the liability was discharged but the corresponding credit was taken in a different period, the annual return will show a difference that must be explained in the reconciliation rather than left to the officer to interpret.
The practical step is to prepare the reconciliation from the trial balance rather than from the returns, so that every difference has a ledger account behind it. A reconciliation built the other way round tends to reconcile to itself and explain nothing.
Last reviewed 26 August 2026.