GSTR-9C Reconciliation Statement FY 2025-26: Filing Walkthrough

Why GSTR-9C Exists and What It Actually Does

If you already file GSTR-9, you might wonder what GSTR-9C adds. The answer: GSTR-9 summarises your return data. GSTR-9C tests whether that return data matches your books of accounts.

Consider a manufacturing company with turnover of Rs 12 crore. Its GSTR-1 filings for the year may show total outward supplies of Rs 11.8 crore. But the audited profit and loss account shows revenue of Rs 12.3 crore. That Rs 50 lakh gap could be advances received but not invoiced, exempt supplies omitted from returns, credit notes that did not flow into GSTR-1, or plain errors in monthly filing. GSTR-9C forces you to identify, explain, and resolve every such gap.

The department uses GSTR-9C data to pick taxpayers for scrutiny and, where tax is found short, demand proceedings (under Section 74A for FY 2024-25 onwards; Sections 73 and 74 apply up to FY 2023-24). A clean, well-reconciled GSTR-9C significantly reduces the probability of a post-filing notice.

Who Must File GSTR-9C for FY 2025-26

Aggregate turnover includes taxable supplies, exempt supplies, exports, and inter-state supplies of all persons sharing the same PAN. It is computed at the PAN level, not the GSTIN level.

If your company has GSTINs in Maharashtra and Karnataka, and the combined turnover across both is Rs 6 crore, you must file GSTR-9C separately for each GSTIN even if neither state's turnover alone exceeds Rs 5 crore.

Who Is Exempt

• Composition dealers (they file the annual return in GSTR-4, not GSTR-9/9C)
• Input Service Distributors (ISD)
• Non-resident taxable persons
• Casual taxable persons
• Persons deducting TDS under Section 51 (government deductors) and e-commerce operators collecting TCS under Section 52
• Foreign airline companies, exempted from GSTR-9C by Notification 09/2020-Central Tax dated 16 March 2020
• Non-resident OIDAR suppliers to unregistered persons in India, exempted by Notification 30/2019-Central Tax dated 28 June 2019

Structure of GSTR-9C: What Goes Where

GSTR-9C is divided into two parts:

Part A is the Reconciliation Statement itself. It has five parts that systematically compare books of accounts against GST returns.

Verification is the self-certification where the authorised signatory declares that the reconciliation is accurate. (The old Part B, the CA or CMA audit certificate, was dropped from FY 2020-21.)

Part I: Basic Details (Tables 1-4)

Tables 1 through 4 capture your GSTIN, legal name, trade name, and the financial year. These are auto-populated from the portal. No manual entry needed.

Part II: Turnover Reconciliation (Tables 5-8)

This is where most of the work happens. The objective is to arrive at the same taxable turnover number from two different starting points: your audited books and your GSTR-9.

Table 5: Turnover as per audited financial statements

Report turnover (including exports) as per the audited annual financial statement for the state or UT of the GSTIN you are filing for. If your entity has multiple GSTINs, you need to internally derive GSTIN-wise turnover from PAN-level financials. This is a manual exercise, and it is where errors start.

Table 6: Reasons for difference between Table 5 and GSTR-9 turnover

This table captures all the adjustments needed to reconcile Table 5 (books turnover) with the turnover declared in GSTR-9. Common line items include:

Table 7: Taxable turnover as per audited financial statement vs as per GSTR-9

After applying Table 6 adjustments, Table 7 should ideally show zero difference. If there is still a gap, it indicates either a filing error in GSTR-9 or a books-of-accounts error. Table 7 also splits the reconciled turnover by tax rate. Because FY 2025-26 spans the GST 2.0 transition (the 12% and 28% slabs were discontinued from September 22, 2025), turnover up to that date may sit in the old slabs (5%, 12%, 18%, 28%) while turnover from September 22 onward uses the current slabs (5%, 18%, 40%). Split the rate-wise breakup by the period in which each supply was made.

Table 7D1 (added from FY 2024-25): This row captures supplies on which tax is payable by the e-commerce operator under Section 9(5) of the CGST Act. It was inserted by Notification 13/2025-Central Tax and applies again for FY 2025-26, so ECO-routed supplies are segregated instead of being mixed with your own taxable turnover.

Table 8: Reasons for unreconciled difference in taxable turnover

If Table 7 still shows a gap after Table 6 adjustments, Table 8 asks you to explain why. This table is conditional: it appears only if Table 7 has unreconciled amounts. Common reasons include GST paid on items not recorded as revenue (penalties, liquidated damages that are GST-liable but not in P&L revenue), and errors in rate classification across returns.

When such a charge is actually taxable is covered in our guide to GST on liquidated damages and penalty charges, which walks through Circular 178.

Part III: Tax Paid Reconciliation (Tables 9-11)

Table 9 compares tax paid as per your audited books (what your books say you owed and paid) against tax paid as declared in GSTR-9. This covers CGST, SGST, IGST, and Cess.

Any difference here typically arises from:

• Interest and late fees paid through GSTR-3B that may or may not be in the books
• Demand orders paid during the year
• Tax on reverse charge inward supplies (if the RCM liability was booked in a different period than when GSTR-3B was filed)

Reasons for any unreconciled difference go in Table 10, and any additional amount payable is shown in Table 11. If you paid less tax in returns than your books indicate you owed, pay the difference through DRC-03 before or along with filing GSTR-9C.

Part IV: ITC Reconciliation (Tables 12-13)

This is the section that takes the most preparation. It compares ITC claimed in GSTR-9 against ITC as per audited financial statements.

Table 12A: ITC as per the audited annual financial statement. This is the total ITC that your audited books say you were entitled to claim during the year.

Table 12B: ITC booked in earlier financial years but claimed in the current year (through GSTR-3B). This amount will not appear in Table 12A (which is current-year books) and will not appear in Table 12E (which is current-year returns). It is a reconciling item.

Table 12C: ITC booked in the current year's books that will be claimed in subsequent financial years. This is deducted to arrive at Table 12D, the ITC availed as per the audited financial statements (12A plus 12B minus 12C).

Table 12E: Auto-populated from Table 7J of GSTR-9. This is the ITC actually claimed in your returns for the current year.

Table 12F: The difference between Table 12D and Table 12E. This is the unreconciled ITC difference.

Table 13: Your explanation for any ITC mismatch. Use this table generously. Document every variance, even expected ones. Common explanations:

• ITC reversed under Rule 42/43 (common credit apportionment for exempt supplies)
• ITC on capital goods claimed proportionally over time
• ITC booked in books but not available in GSTR-2B (supplier did not file, or invoice was not uploaded)
• ITC claimed in returns but reversed in books after an internal audit

Part V: Additional Liability Due to Non-Reconciliation

This part captures any additional liability identified during the reconciliation, such as under-reported turnover or over-claimed ITC. Under the old CA-certified format it was the auditor's recommendation; under self-certification the authorised signatory reports the payable amount, which must be discharged through DRC-03.

Table 17: Late Fee Payable and Paid (from FY 2024-25)

Circular 246/03/2025-GST dated 30 January 2025 clarified that late fee under Section 47(2) applies to delay in furnishing the complete annual return, which includes GSTR-9C where it is required. From FY 2024-25 a new Table 17 below Part V of GSTR-9C captures this. The portal computes late fee from the date of filing GSTR-9 or the due date, whichever is later, until the date GSTR-9C is filed. For example, if GSTR-9 is filed on time on 20 December 2026 and GSTR-9C on 7 January 2027, late fee for 7 days is auto-populated in GSTR-9C.

The Self-Certification Process

Since FY 2020-21, the Finance Act, 2021 (Sections 110 and 111, brought into force from 1 August 2021 by Notification 29/2021-CT dated 30 July 2021) replaced mandatory CA audit certification with self-certification by the taxpayer. Rule 80(3) was amended accordingly by Notification 30/2021-CT of the same date.

What this means in practice:

• The authorised signatory of the registered person (director, partner, proprietor, or authorised representative) certifies the reconciliation statement.
• No CA or CMA is required to sign or certify the form.
• No UDIN (Unique Document Identification Number) is generated or required on the GST portal for GSTR-9C.
• The self-certification is a legal declaration that the reconciliation is true and correct to the best of the signatory's knowledge. Incorrect declarations can attract proceedings under Section 122 (penalties for incorrect information) and Section 132 (offences and prosecution) of the CGST Act.

This does not mean you should not involve your CA. Most businesses above Rs 5 crore turnover already have statutory auditors. The reconciliation work is a natural extension of the annual audit. What changed is that the CA no longer needs to formally certify GSTR-9C on the portal.

How to Prepare: A Practical Checklist

The December scramble happens because businesses treat GSTR-9C as a December task. It is not. Reconciliation should begin the moment your statutory audit is complete (typically September-October for most companies).

Step 1: Get Your GSTR-9 Right First

GSTR-9C reconciles against GSTR-9, not against monthly returns. If your GSTR-9 itself has errors, your GSTR-9C reconciliation will cascade those errors into unexplainable variances. Read our GSTR-9 annual return guide and ensure your GSTR-9 is accurate before touching GSTR-9C.

Step 2: Prepare a GSTIN-Wise Trial Balance

Your audited financials are at the PAN level. GSTR-9C is at the GSTIN level. If you have multiple GSTINs, split your revenue, purchases, and ITC GSTIN-wise before you start. This step is manual and often the most time-consuming.

Step 3: Reconcile Turnover

• Extract total revenue from the P&L for the GSTIN.
• Subtract non-GST revenue (for example, interest and dividend income).
• Add deemed supplies under Schedule I that are GST supplies but not P&L revenue.
• Add advances for services on which GST was paid but which are not yet revenue in the P&L, and subtract unbilled revenue that is in the P&L but not yet invoiced.
• The result should match your GSTR-9 turnover. If it does not, document every difference in Table 6.

Step 4: Reconcile ITC

• Extract ITC claimed in GSTR-3B for the year (Table 4 of GSTR-3B, summed for 12 months or from GSTR-9 Table 7J).
• Compare against ITC in your purchase register or books.
• Common mismatches: invoices booked in books but not in GSTR-2B (supplier non-filing), ITC reversed under Rule 42/43, ITC on capital goods proportioned across years, ITC claimed in a different year than booked.
• Document every variance in Table 13.

Step 5: Reconcile Tax Paid

• Compare tax liability per books (output tax on revenue) against tax declared in GSTR-9.
• Check RCM liability (Section 9(3) and 9(4)) timing: was RCM paid in the month of accrual or a different month?
• Reconcile interest and late fees.

Step 6: Pay Any Differential Through DRC-03

If the reconciliation reveals under-payment of tax or over-claim of ITC, pay the differential through Form DRC-03 on the GST portal before filing GSTR-9C. Report the payment against the additional liability in Part V of GSTR-9C and keep the DRC-03 ARN on file.

Step 7: File and Self-Certify

• Log in to the GST portal. Navigate to Annual Return, select FY 2025-26.
• GSTR-9C can be filed only after GSTR-9 for that GSTIN has been filed.
• Fill Parts II to V based on your reconciliation workpapers.
• Review Table 17 (auto-calculated late fee, if any).
• Self-certify through DSC or EVC and submit.

Common Mistakes That Trigger Notices

1. Not splitting PAN-level financials GSTIN-wise. The department matches GSTR-9C table 5 against GSTR-9 at the GSTIN level. If you dump PAN-level revenue into one GSTIN's GSTR-9C, the other GSTINs will show zero turnover in 9C but non-zero turnover in GSTR-9.

2. Ignoring Table 12B (prior-year ITC claimed in current year). This creates a permanent mismatch between Table 12A and Table 12E that looks like over-claimed ITC to the department. Always populate Table 12B for prior-year ITC.

3. Forgetting deemed supplies. Stock transfers to another GSTIN under the same PAN are GST supplies (Schedule I, Entry 2) even though they are not P&L revenue. They must appear in the GSTR-9C turnover reconciliation.

4. Not paying DRC-03 before filing. If your reconciliation reveals additional liability, the department expects you to pay through DRC-03 and reference the ARN. Filing GSTR-9C with an admitted liability but no DRC-03 payment is an invitation for a demand notice under Section 74A.

5. Leaving Table 13 empty. Even if the differences are small and expected (rounding, timing), document them. An empty Table 13 with a non-zero Table 12F tells the department you did not bother to investigate the mismatch.

Penalties and Consequences

Source Attribution

The rules governing GSTR-9C are found in Section 44 of the CGST Act, 2017 read with Rule 80 of the CGST Rules, 2017. The turnover threshold of Rs 5 crore was set by CBIC Notification 30/2021-Central Tax dated 30 July 2021. The shift from CA certification to self-certification was enacted through the Finance Act, 2021, brought into force by Notification 29/2021-CT dated 30 July 2021. The Rs 2 crore GSTR-9 exemption from FY 2024-25 is under Notification 15/2025-CT, the FY 2024-25 form changes (including Tables 7D1 and 17 of GSTR-9C) under Notification 13/2025-CT dated 17 September 2025, and the GSTR-9C late fee position under Circular 246/03/2025-GST. Exemptions for foreign airlines and OIDAR providers are governed by Notifications 09/2020 (16 March 2020) and 30/2019 (28 June 2019) respectively. The general penalty for non-compliance is under Section 125 of the CGST Act.