GST Annual Return GSTR-9 and Reconciliation Statement GSTR-9C — Who Must File (₹2 Crore and ₹5 Crore Thresholds), Table by Table, Reconciling Books to Returns, Paying Differences Through DRC-03, Late Fees, and What a Departmental GST Audit Looks Like
₹2 crore
Aggregate turnover above which GSTR-9 is mandatory (optional below)
₹5 crore
Aggregate turnover above which the self-certified GSTR-9C must accompany GSTR-9
31 Dec
Due date for both, for the previous financial year
0.04% / 0.5%
Late-fee caps as a percentage of turnover in the state, by turnover band
Guide by BookMyCA's Chartered Accountants · pan-India serviceLast verified against official guidelines on 6 September 2026.
Video Explanation & Insights
GST audit: reconciliation, thresholds and what gets checked
4 videos on this topic
Who files what
| Aggregate turnover in the FY (PAN-wide) | GSTR-9 | GSTR-9C |
|---|---|---|
| Up to ₹2 crore | Optional (exempted by notification each year) | Not required |
| ₹2 crore to ₹5 crore | Mandatory | Not required |
| Above ₹5 crore | Mandatory | Mandatory, self-certified by the taxpayer (no CA certification since FY 2020-21) |
| Composition dealers | GSTR-4 annual instead; GSTR-9A waived | — |
| Casual taxable persons, non-residents, ISD, TDS/TCS deductors, OIDAR | Not required | — |
Every GSTIN files its own GSTR-9; the ₹2 crore and ₹5 crore tests are on the PAN-level aggregate turnover, so a small branch in one state files because the company as a whole crosses the limit.
GSTR-9 — the tables that decide the outcome
| Table | Content | What to check |
|---|---|---|
| 4 | Outward supplies on which tax is payable, as declared in the year's returns (B2B, B2C, exports with tax, SEZ, RCM inward, credit/debit notes, amendments) | Should equal the books after adding sales reported in the next year's returns (Table 10/11) |
| 5 | Outward supplies on which tax is not payable — exports under LUT, exempt, nil-rated, non-GST | LUT exports must match shipping bills |
| 6 | ITC availed, split by inputs, input services and capital goods, plus RCM and import credit | 6A auto-fills from GSTR-3B; the split must be from books |
| 7 | ITC reversed — rules 37, 39, 42, 43, section 17(5), others | Reversals made in the next year go to Table 12 |
| 8 | ITC as per GSTR-2A/2B (8A auto), availed (8B), lag claims (8C), difference (8D) — the 'ITC lapsed' table | 8D should be explainable: supplier-side timing, ineligible credit, or genuinely lapsed |
| 9 | Tax paid — as per returns, cash and credit | Ties to GSTR-3B Table 6.1 totals |
| 10–13 | Transactions of the year reported in the returns of April–November of the next year | Sales and credit notes reported late; ITC claimed late |
| 14 | Differential tax paid on account of Tables 10 and 11 | Pay through DRC-03 before filing |
| 15–16 | Demands and refunds; supplies from composition dealers, deemed supplies, goods sent on approval | Optional/relaxed in most years |
| 17–18 | HSN-wise summary of outward (mandatory) and inward supplies | 4-digit for turnover up to ₹5 crore, 6-digit above; matches GSTR-1 Table 12 |
GSTR-9C — reconciling the audited accounts to GST
- 1Part A, Table 5: start from the audited turnover of the entity, allocate it to the GSTIN, and adjust for unbilled revenue, advances, credit notes, deemed supplies, trade discounts, non-GST income and the timing differences between books and returns to reach the turnover declared in GSTR-9.
- 2Table 6–8: explain every unreconciled turnover difference and reconcile the taxable turnover rate-wise; Table 9 reconciles tax paid by rate.
- 3Table 12–14: reconcile the ITC in the books (expense-head-wise, Table 14 is optional in most years) with the ITC availed in GSTR-9; unexplained differences become additional liability or lapsed credit.
- 4Part B: self-certification by the taxpayer (verification with DSC or EVC) — the auditor's Part B was removed by the Finance Act 2021 from FY 2020-21.
- 5Pay any additional liability arising from the reconciliation through DRC-03 (select 'Annual Return' as the cause) before filing; interest applies from the original due dates.
Due date, late fee and the three-year bar
| Turnover band | GSTR-9 late fee per day | Cap |
|---|---|---|
| Up to ₹5 crore | ₹50 (₹25 CGST + ₹25 SGST) | 0.04% of turnover in the state (0.02% + 0.02%) |
| ₹5 crore to ₹20 crore | ₹100 | 0.04% of turnover in the state |
| Above ₹20 crore | ₹200 | 0.5% of turnover in the state (0.25% + 0.25%) |
- •GSTR-9C attracts no separate late fee, but GSTR-9 is treated as incomplete until 9C is filed where it is mandatory, and the general penalty under section 125 (₹25,000 + ₹25,000) can be invoked.
- •The late-fee amnesty for FY 2017-18 to 2022-23 annual returns (₹20,000 cap, filed by 31 March 2025) has closed.
- •Since 1 August 2025 an annual return more than three years past its due date cannot be filed — FY 2020-21 (due 28 February 2022) and earlier are now barred.
- •GSTR-9 cannot be filed until every GSTR-1 and GSTR-3B of the year is filed; it cannot be revised, so reconcile before filing.
Departmental audit and special audit
- •Section 65 audit: the Commissioner may audit any registered person for a financial year or part; 15 working days' notice in ADT-01, completion within 3 months (extendable by 6), findings in ADT-02; typically covers turnover reconciliation, ITC eligibility, RCM, e-way bills, classification and valuation.
- •Section 66 special audit: ordered during scrutiny or investigation when values or credits look wrong, conducted by a CA or CMA nominated by the Commissioner within 90 days, at the department's cost.
- •Selection is data-driven: GSTR-9 vs GSTR-3B mismatches, Table 8D credit gaps, high refund claims, ITC from suppliers with cancelled registrations, income-tax turnover vs GST turnover, and TDS/TCS data.
- •Preparation: monthly reconciliations filed in a binder, supplier-wise ITC ledger with GSTR-2B matches, e-way bill and e-invoice registers, RCM self-invoices, fixed-asset register for capital-goods credit, and the DRC-03 trail for every voluntary payment.
- •After findings: pay with interest and 15% penalty before the show-cause notice (section 73/74A) to close at the lowest cost; disputed points go to the adjudication and appeal route.
GSTR-9 and 9C: questions we are asked
It is optional below ₹2 crore, but filing it closes the year formally and is advisable where you have differences to disclose or refunds pending.
No. GSTR-9C is self-certified since FY 2020-21; a CA's role is preparing the reconciliation and advising on the differences.
Declare them in Table 4 or Table 10 (if reported in the next year's returns), pay the tax and interest through DRC-03 before filing.
No — GSTR-9 only reports credit already claimed in GSTR-3B. Credit not claimed within the section 16(4) limit lapses.
The gap between credit available in GSTR-2A/2B and credit claimed; a large positive figure is credit you did not take, a negative figure invites a notice.
Yes — reconciliation, GSTR-9, GSTR-9C, DRC-03 payments and representation in departmental audits.