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Indirect Tax Services

GSTR-9 Annual Return & GSTR-9C Reconciliation

GSTR-9 / 9C

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Regulatory Framework

GSTR-9C is the annual reconciliation statement required under Section 44 of the CGST Act, 2017 read with Rule 80(3) of the CGST Rules, 2017. It reconciles the values declared in the taxpayer's annual return (GSTR-9) — turnover, tax paid, and Input Tax Credit availed — against the corresponding figures in the taxpayer's audited annual financial statements for the financial year.

Applicability is turnover-based: every registered person (other than an Input Service Distributor, a person paying tax under Section 51 (TDS) or Section 52 (TCS), a casual taxable person, or a non-resident taxable person) whose aggregate turnover during the financial year exceeds ₹5 crore must furnish GSTR-9C along with GSTR-9. This ₹5 crore threshold was fixed by amendment to Rule 80(3), raised progressively from an original ₹2 crore threshold in the early years of GST.

A significant procedural change took effect from FY 2020-21 onward (given legal effect via the Finance Act, 2021 and a corresponding CBIC notification effective 01.08.2021): the earlier requirement of certification by a practising Chartered Accountant or Cost Accountant was removed, and GSTR-9C is now filed on a self-certification basis by the taxpayer (typically the authorized signatory/proprietor/partner/director), rather than by an independent auditor.

The due date for filing GSTR-9C, filed electronically on the GST common portal along with GSTR-9, is 31 December following the end of the relevant financial year, unless extended by the Government/GST Council for a specific year. Non-filing where applicable attracts a late fee under Section 47 and exposes the taxpayer to scrutiny/audit action under Sections 65/66.

Overview

GSTR-9 and GSTR-9C are the annual return and the reconciliation statement that close a registered business's GST year. Under Section 44 of the CGST Act 2017 and Rule 80 of the CGST Rules, the GSTR-9 consolidates the year's outward supplies, credit and tax paid, and the GSTR-9C reconciles the turnover and the tax declared in the returns with the audited annual financial statements — with the certification by the chartered accountant or the self-certification where the turnover is below the threshold under the Rules. The annual filing is the year's final declaration.

The annual return is where the year's positions are finally reconciled — and where the year's mistakes surface. The monthly returns are filed on the run; the GSTR-9 and the GSTR-9C are the year in review, and the reconciliation between the books and the returns is the test the year's compliance must pass. The differences the reconciliation finds — the exempt supplies, the reversals, the rate changes, the ineligible credits — are the seeds of the future notices if they are not resolved.

The cost of a perfunctory annual filing is the accumulated exposure: the GSTR-9C that certifies a reconciliation that was never done, the differences that surface in the scrutiny and the audits as the demands with interest, and the year that is re-opened because the annual filing did not reflect the records. The annual filing is the cheapest place to find the year's problems.

This service is for businesses required to file the annual return. We reconcile the year's returns with the audited financial statements under Rule 80, prepare and file the GSTR-9 under Section 44, prepare the GSTR-9C with the reconciliation workings and the certification, and resolve the differences between the books and the returns — so the year closes clean and the next year starts clean.

How It Works

  1. 1

    Year's Data Consolidation

    We consolidate the year's returns, ledgers and audited statements.

    Harun Raaj & Associates does this1 week
  2. 2

    Reconciliation Workings

    We build the reconciliation between the books and the returns under Rule 80.

    Harun Raaj & Associates does this1-2 weeks
  3. 3

    GSTR-9 Filing

    We prepare and file the GSTR-9 under Section 44.

    Harun Raaj & Associates does this1 week
  4. 4

    GSTR-9C & Certification

    We prepare the GSTR-9C with the certification and the workings.

    Harun Raaj & Associates does this1 week
  5. 5

    Difference Resolution & Close

    We resolve the differences found and close the year's compliance.

    Harun Raaj & Associates does this1-2 weeks

Frequently Asked Questions

Who is required to file GSTR-9C and what is the aggregate turnover threshold?
GSTR-9C is a reconciliation statement that must be filed by every registered taxpayer whose aggregate annual turnover in a financial year exceeds Rs 5 crore, as notified by the Government under Section 44 of the CGST Act 2017 read with Rule 80(3) of the CGST Rules 2017, as amended by Notification No. 30/2021-CT dated August 30, 2021. Prior to Financial Year 2020-21, GSTR-9C required certification by a Chartered Accountant or Cost Accountant; from FY 2020-21 onwards, it is a self-certified reconciliation statement filed by the taxpayer themselves, though CA assistance remains critical given the complexity of reconciliation. Taxpayers below Rs 5 crore turnover are exempt from GSTR-9C but must still file GSTR-9 (annual return). Composition scheme taxpayers file GSTR-9A (suspended currently) and are exempt from GSTR-9C.
What are the key reconciliation points between GSTR-9 and GSTR-9C that commonly result in discrepancies?
The primary reconciliation in GSTR-9C involves Table 5 (reconciliation of gross turnover declared in audited financials versus GST returns), Table 7 (reconciliation of ITC as per audited accounts versus ITC claimed in GSTR-3B), and Table 12 (reconciliation of ITC on inward supplies per books vs GSTR-2A/2B). Common discrepancies arise from advances received treated differently in books versus GST returns under Section 12 of the CGST Act 2017, export turnover under Section 16 of the IGST Act 2017 included in financial turnover but excluded from taxable GST turnover, and ITC reversals under Rule 42 (inputs used for exempt and taxable supplies) not fully reflected in GSTR-3B. Discrepancies in Table 7 (ITC difference) require payment of additional tax with interest under Section 50(1) of the CGST Act 2017 at 18% per annum if unpaid GST is identified.
What is the due date for GSTR-9 and GSTR-9C, and what are the late filing fees?
Both GSTR-9 and GSTR-9C must be filed by December 31 following the close of the financial year under Section 44 of the CGST Act 2017, though the Government has typically extended this deadline by notification each year (e.g., Notification No. 07/2025-CT extended FY 2023-24 deadline). Late filing of GSTR-9 attracts a late fee of Rs 200 per day (Rs 100 under CGST + Rs 100 under SGST) under Section 47 of the CGST Act 2017, subject to a maximum of 0.25% of turnover in the State or Union Territory. GSTR-9C does not carry a separate late fee but cannot be filed without a valid GSTR-9 filing, so the GSTR-9 late fee applies to both. Non-filing can also lead to demand and recovery proceedings under Section 73 or Section 74 for any tax differences identified.
Can errors in GSTR-1 or GSTR-3B discovered during annual return preparation be corrected in GSTR-9?
GSTR-9 allows taxpayers to declare additional liability for any supplies not declared or short-declared in GSTR-1/GSTR-3B during the financial year, effectively paying the differential tax through the GSTR-9 filing — this is governed by Section 44 read with Rule 80(1) of the CGST Rules 2017. Similarly, ITC that was missed in GSTR-3B can be availed up to the due date of filing GSTR-3B for September of the subsequent financial year (now linked to GSTR-9 filing deadline per Section 16(4) of the CGST Act 2017, as amended by the Finance Act 2022). However, GSTR-9 cannot be used to reduce previously declared output tax liability — that requires filing of an amendment return or rectification, and excess ITC claimed can only be reversed in GSTR-3B. The GSTN portal auto-populates GSTR-9 tables from filed returns but all figures remain editable by the taxpayer.
What documentation should we retain to support the GSTR-9C reconciliation in case of a GST audit or scrutiny?
Taxpayers should retain the audited financial statements, trial balance, ledger-wise GST output tax accounts, and input tax credit registers reconciled to GSTR-2B for each month of the financial year, as these form the basis of the GSTR-9C reconciliation under Rule 80(3) of the CGST Rules 2017. For ITC reconciliation (Table 12), month-wise GSTR-2B downloads, vendor invoices, and the purchase register with HSN-wise bifurcation should be maintained for at least 6 years as required under Section 36 of the CGST Act 2017. For turnover reconciliation, export documentation (shipping bills, FIRC) and advance receipt vouchers with time-of-supply calculations under Section 12 and 13 of the CGST Act 2017 should be preserved. In case of a GST audit under Section 65, the officer may requisition these records within 5 working days' notice and failure to produce them constitutes an offence under Section 122(1)(ix).

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