Since the amendment effective from financial year 2020-21, taxpayers above the prescribed aggregate turnover threshold file GSTR-9C as a self-certified reconciliation statement between the audited financial statements and the annual return, without a mandatory certification by a chartered or cost accountant — but the reconciliation itself, and the turnover threshold above which GSTR-9C applies at all, are still in force, and a statutory auditor should check the threshold was correctly assessed and that the self-certified reconciliation is supportable from the entity's own records even without being asked to certify it.
What the amendment actually changed
- The requirement for a chartered accountant or cost accountant to certify GSTR-9C was removed for most taxpayers; the taxpayer now self-certifies the statement instead.
- The requirement to file GSTR-9C itself, above the prescribed aggregate turnover threshold for the financial year, continues — self-certification is a change in who signs, not whether the filing is required.
- The reconciliation content GSTR-9C asks for — turnover reconciled between the audited financial statements and the annual return, tax paid reconciled, and input tax credit reconciled — is unchanged in substance.
What the statutory auditor should still check
| Check | Why it still matters | Evidence |
|---|---|---|
| Turnover threshold assessment | Determines whether GSTR-9C is even required for the year | Aggregate turnover computation across all GSTINs under the same PAN |
| Turnover reconciliation accuracy | The reconciliation draws directly on figures the statutory audit has already tested | Audited financial statements, GSTR-9 annual return |
| Self-certification doesn't mean unreviewed | A self-certified statement filed with unreconciled differences still exposes the entity to a departmental query | GSTR-9C working papers maintained by the client |
| Consistency with the statutory financials | A reconciliation statement that disagrees with the audited numbers is itself a red flag worth raising | Comparison of GSTR-9C turnover figures to the audited P&L |
Regulatory requirement
The aggregate turnover threshold above which GSTR-9C applies, and the self-certification requirement replacing mandatory CA/CMA certification, were introduced by amendment effective from FY 2020-21. Confirm the threshold in force for the year under audit, since turnover thresholds for GST filings are periodically revisited.
How we think about this
Removing the mandatory certification removed a formal attestation step, not the underlying reconciliation risk. Where the statutory audit already has the data to sanity-check the GSTR-9C turnover figures against the audited financials, doing that check costs little and catches a filing inconsistency before it becomes a departmental notice.
This is practical guidance written for audit teams, not an authoritative statement of any standard or statute. Standards, forms and timelines change. Check the current text issued by the ICAI and the relevant authority before relying on anything here in an audit file.
Related resources
- GST & GSTR-2BGSTR-2B reconciliation: a practical guide for auditorsWhat GSTR-2B is, how the Invoice Management System changed it, the statutory conditions that govern input credit, and how to run and conclude the reconciliation.
- GST & GSTR-2BGSTR-3B vs GSTR-1 reconciliation for auditorsWhy GSTR-1 and GSTR-3B outward-supply figures disagree, the usual causes, and what to do with a difference still unreconciled at the year end.
- GST & GSTR-2BTwelve GST reconciliation mistakes that show up in audit filesPooling registrations, reconciling against 2A, stopping at March, netting categories and eight more errors, with what each causes and how to correct it.
- Revenue, receivables & cut-offMatching dispatch, invoice and ledger for revenue testingThe sales-side mirror of the purchase three-way match: what breaks it in practice, and why the unmatched population should be sized by value, not count.
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