Who must file GSTR-9C
A registered person whose aggregate annual turnover in the financial year exceeds ₹5 crore. The threshold and the form both come from Rule 80(3) of the CGST Rules, as amended by Notification 30/2021-Central Tax of 30 July 2021.
It is filed with the annual return, after GSTR-9 and on the same portal. The taxpayers who are outside GSTR-9 altogether are also outside GSTR-9C: a composition taxpayer, who files GSTR-4 by 30 June instead, an input service distributor, a person deducting or collecting tax under section 51 or section 52, a casual taxable person and a non-resident taxable person. That list, the GSTR-9 tables and the graded late fee all sit on GSTR-9 annual return filing.
The ₹5 crore test is PAN level, the form is GSTIN level
This is the point that catches multi-state businesses.
Aggregate turnover is a PAN-level figure. It adds up the turnover of every GSTIN under the same PAN across India. So a business with three registrations turning over ₹2 crore each has aggregate turnover of ₹6 crore and is above the line, even though no single registration is anywhere near ₹5 crore.
GSTR-9C is then filed per GSTIN. Three registrations means three statements, three reconciliations and three sets of explanations, prepared from one set of audited accounts that has to be split by GSTIN first. Your audited financial statements are drawn up at entity level, so the split is the first piece of work, not the last.
| You have | Aggregate turnover | GSTR-9C |
|---|---|---|
| One GSTIN, turnover ₹4 crore | ₹4 crore | Not required |
| One GSTIN, turnover ₹8 crore | ₹8 crore | One statement |
| Three GSTINs at ₹2 crore each | ₹6 crore | Three statements, one per GSTIN |
| Two GSTINs, ₹5.5 crore and nil | ₹5.5 crore | Two statements, including one for the nil registration |
GSTR-9C is self-certified, and what that changed
Since FY 2020-21 you certify it yourself. There is no certificate from a chartered accountant or a cost accountant.
Up to FY 2019-20 the form had two parts: Part A, the reconciliation statement, and Part B, the certificate signed by an auditor. Notification 30/2021-Central Tax omitted Part B. What is left is Part A, and you sign it.
Two practical consequences follow, and they pull in opposite directions.
- The compliance step got cheaper and faster, because no separate audit and certificate is needed.
- The exposure moved onto you. Nobody now reviews the reconciliation before it is filed unless you arrange it. A self-certified statement with an unexplained gap in Table 5 or Table 12 is your statement, and it is read by an officer who has your GSTR-1, your GSTR-3B and your GSTR-2B already.
Most businesses above ₹5 crore still have the reconciliation prepared by a CA, not because the law requires a signature, but because the statement is an admission of differences and it is safer to find them first. That is what this service is.
GSTR-9C due date
31 December 2026 for FY 2025-26. The rule is 31 December following the end of the financial year, unless the government extends it by notification. Put it on your compliance calendar.
GSTR-9C is filed after GSTR-9, and the portal opens it only once all your GSTR-1 and GSTR-3B returns for the year have been filed. Neither GSTR-9 nor GSTR-9C can be revised after filing, so the review has to happen before you certify. For the due date history, extensions and the late fee slabs, see GSTR-9 annual return filing.
The five parts of GSTR-9C
Five parts, tables numbered 5 to 16, with the basic details in Part I.
| Part | What it does | Tables |
|---|---|---|
| Part I | Basic details: financial year, GSTIN, legal and trade name | 1 to 4 |
| Part II | Reconciles turnover in the audited annual financial statement with turnover declared in the annual return | 5 to 8 |
| Part III | Reconciles tax paid | 9 to 11 |
| Part IV | Reconciles input tax credit | 12 to 16 |
| Part V | Additional liability arising from the differences that could not be reconciled |
The shape tells you what the form is for. Each of Parts II, III and IV has a reconciliation table, then a table where you write the reasons for the difference that remains, then, in Parts III and IV, a table for the tax payable on it. The form is designed so that a difference you cannot explain becomes a payment.
Part II: reconciling turnover (Tables 5 to 8)
Turnover in the accounts, adjusted step by step until it equals turnover in the annual return.
| Table | Heading | What it asks for |
|---|---|---|
| 5 | Reconciliation of gross turnover | Turnover per the audited accounts, then the adjustments: turnover of other GSTINs under the same PAN, unbilled revenue at the start and end of the year, unadjusted advances, deemed supplies, credit notes issued after the year end, trade discounts not allowable, the part-year effect for the first year of registration, and the rest |
| 6 | Reasons for un-reconciled difference in annual gross turnover | Free text for whatever Table 5 could not absorb |
| 7 | Reconciliation of taxable turnover | Gross turnover reduced to taxable turnover: exempt, nil-rated and non-GST supplies, zero-rated supplies without payment of tax, and supplies on which the recipient pays under reverse charge |
| 8 | Reasons for un-reconciled difference in taxable turnover | Free text again |
Table 5 is where most of the work sits, because the audited accounts are prepared on accounting principles and GST turnover is a statutory concept. Revenue recognised but not invoiced, invoices raised for a supply that has not happened, and stock moved between your own registrations in different states are all differences by design, not errors.
Tables 5B to 5F were made optional for the years FY 2017-18 to FY 2022-23, with the adjustments allowed to be shown in Table 5O instead. That relaxation does not cover FY 2025-26, so the individual rows are filled.
Part III: reconciling tax paid (Tables 9 to 11)
Tax payable on the reconciled taxable turnover, rate by rate, against tax actually paid.
| Table | Heading | What it asks for |
|---|---|---|
| 9 | Reconciliation of rate wise liability and amount payable thereon | Taxable value and tax at each rate, including reverse charge, interest, late fee and penalty, against the total paid per the annual return |
| 10 | Reasons for un-reconciled payment of amount | The explanation for the gap |
| 11 | Additional amount payable but not paid | Rate-wise, the tax you now accept is short |
Table 9 is the table that exposes a classification problem. If a supply was taxed at the wrong rate, the value reconciles and the tax does not, and the difference lands here with no place to hide.
Part IV: reconciling input tax credit (Tables 12 to 16)
Two separate reconciliations of credit, which is why this part is the longest.
| Table | Heading | What it asks for |
|---|---|---|
| 12 | Reconciliation of net input tax credit | Credit availed per the audited accounts, adjusted for credit booked in earlier years but claimed this year and the reverse, against credit claimed in the annual return |
| 13 | Reasons for un-reconciled difference in ITC | The explanation |
| 14 | Reconciliation of ITC declared in the annual return with ITC availed on expenses | Expense head by expense head: purchases, freight, power and fuel, rent, repairs, insurance, professional fees and the rest, with the eligible credit against each |
| 15 | Reasons for un-reconciled difference in ITC | The explanation for Table 14 |
| 16 | Tax payable on un-reconciled difference in ITC | The credit you now accept was not available |
Table 14 is the one businesses underestimate. It forces you to look at credit by expense head rather than in total, which means your expense ledgers have to be mapped to GST treatment: eligible, blocked, partly eligible, or reverse charge. If nobody did that mapping through the year, it is done in December under deadline pressure.
Ten differences that show up in the reconciliation
These are the recurring ones. Finding them in your own file is cheaper than being asked about them.
- Turnover of other GSTINs. The accounts are at entity level, the statement is per GSTIN, and the split has to tie back.
- Unbilled revenue. Revenue accrued at one year end and invoiced in the next, at both ends of the year.
- Advances. Money received with no invoice raised, and its treatment at the year end.
- Deemed supplies. Stock transferred between your own registrations in different states, and supplies to related parties, are supplies under Schedule I even with no money changing hands.
- Credit notes and discounts. A discount reduces taxable value only where the conditions in section 15(3)(b) are met. A commercial credit note that does not meet them reduces your books and not your GST turnover.
- Income sitting in "other income". Scrap sales, sale of an asset, rent received and similar items are supplies even though the accounts do not show them as revenue.
- Exempt, nil-rated and non-GST supplies mixed together. Table 7 needs them apart, and most trial balances do not keep them apart.
- Reverse charge. Supplies on which the recipient pays are turnover in your books but come out of your taxable turnover, and your own inward reverse charge liability sits in Table 9.
- Credit availed across years. Credit of the previous year taken in this one, and credit of this year taken in the next, both belong in Table 12.
- Reversals under Rule 42 and Rule 43. Where you have exempt supplies or common credit, the reversal has to be computed and shown, not left to the auto-populated figure.
If a difference has already produced a notice for an earlier year, see GST notice reply.
What FY 2025-26 adds: the September 2025 rate change
One extra reconciliation this year, and it shows up in Table 9.
From 22 September 2025 the main GST rates became 5% and 18%, with 40% for demerit goods. FY 2025-26 therefore contains supplies at the old rates up to 21 September 2025 and at the new rates from 22 September 2025, and Table 9 is rate-wise.
Two places go wrong. Supplies invoiced after 22 September 2025 but taxed at the old rate, and credit notes or amendments issued after the change against invoices raised before it. Both leave a rate-wise gap that reconciles in value and not in tax. We split the year at 21 and 22 September before building Table 9, rather than after the totals refuse to agree.
What you do with an unexplained difference
You accept it and pay, or you explain it and document it. Leaving the row blank is the one option that is not available.
Where the reconciliation shows extra tax, it is paid through DRC-03 with interest at 18% a year under section 50(1). The additional liability in Part V and in Tables 11 and 16 is what you are accepting, so it should match what you have paid.
Where the difference is genuine and explainable, the reasons tables exist for exactly that. Write the reason in the form, and keep the working behind it: the ledger extract, the reconciliation sheet, the invoice list. A reason with no working behind it is the thing an officer asks about first.
Documents we need
- Audited financial statements for FY 2025-26, and the trial balance, see statutory audit
- GSTIN-wise turnover split, or the ledgers from which we can build it
- GSTR-1, GSTR-3B and GSTR-2B for all twelve months, for every GSTIN
- The GSTR-9 draft, or the working if GSTR-9 is not filed yet
- Expense ledgers mapped to expense heads, for Table 14
- Credit and debit note registers, with the reason for each
- Details of stock transfers between your own registrations
- Rule 42 and Rule 43 reversal workings, where you have exempt or common supplies
- Any DRC-03 already paid for the year, and any notice received
Fees
Fee on quote after a free review. There is no government fee to file GSTR-9 or GSTR-9C on time.
| Item | Position |
|---|---|
| Regikart professional fee, GSTR-9C | From ₹7,499 per GSTIN, as published on GSTR-9 annual return filing. Final fee on quote after a free review |
| Regikart professional fee, GSTR-9 | From ₹4,999 per GSTIN, see GSTR-9 annual return filing |
| Government fee | No government fee |
| Late fee on the annual return | Charged by the portal if you file late, at the graded slabs on GSTR-9 annual return filing |
| Monthly GST returns | See GST return filing |
Professional fees exclude GST at 18%. Government fees, where they apply, are paid at actuals to the department and are shown separately. Fees verified on 27 September 2026.
What moves the quote: the number of GSTINs, the number of expense heads to be mapped for Table 14, whether the GSTIN-wise split already exists, transaction volume, and whether the monthly returns were reconciled during the year or not at all.
How we prepare and file it
- Split the accounts by GSTIN. Everything else depends on this, and it is the step clients most often have not done.
- Build Table 5 and Table 7. Gross turnover to GST turnover to taxable turnover, with every adjustment traced to a ledger.
- Build Table 9 rate-wise, with the year split at the 22 September 2025 rate change.
- Map expenses for Tables 12 and 14, head by head, with eligible, blocked and reverse-charge credit separated.
- List the differences and decide each one: explainable with working, or payable. Nothing is left as an unexplained residual.
- Pay through DRC-03 where tax is short, with interest, before filing.
- File GSTR-9, then GSTR-9C, and hand over the working papers so the same file supports you if a notice arrives two years later.
Why businesses above ₹5 crore bring this to Regikart
Regikart is a CA and CS firm serving 250+ clients, with offices in Kolkata (head office), Delhi and Bengaluru. This page is reviewed by CA Deepak Jaiswal.
- A review before you self-certify. The certificate is gone, so the review is the value. We do the work a Part B audit used to force.
- Multi-GSTIN work handled properly. One set of audited accounts, split and reconciled per registration, with the split documented.
- Working papers you keep. A notice on FY 2025-26 can arrive well after filing, and the file is what answers it. See GST notice reply.
- The rest of the GST stack in the same firm. Monthly returns, refunds, e-invoicing and appeals.