Every business crossing the ₹2 crore turnover mark in a financial year faces a quiet but serious obligation under the CGST Act 2017: a mandatory GST audit, culminating in the filing of Form GSTR-9C on the GST portal. Yet most MSMEs discover the scope of this obligation only when the December 31 deadline is weeks away, or worse, when a notice arrives from the jurisdictional GST officer asking why GSTR-9C was not filed. The consequences are not academic. Failure to file GSTR-9C attracts a flat penalty of ₹20,000 under Section 125 of the CGST Act 2017, and the absence of a clean reconciliation statement means input tax credit (ITC) mismatches that could be worth lakhs go undetected until a departmental scrutiny or audit. KAMRIT Financial Services LLP offers a structured GST Audit and Health Check engagement that takes you from raw GSTR-1, GSTR-3B and GSTR-9 data to a verified, auditor-certified GSTR-9C filing, with a written health check report that flags ITC gaps, exemption errors, HSN misclassifications and reverse charge anomalies before the tax department finds them first. Our engagement covers the full cycle: pre-filing reconciliation, statutory audit procedures under Rule 80(1) of the CGST Rules 2017, draft report review, client sign-off and portal filing. You get a qualified chartered accountant sign-off, not a software-generated export.
What is GST Audit in India 2026?
A GST Audit under the Indian GST framework is a two-part statutory exercise. First, the registered person must self-prepare and file the annual return in Form GSTR-9 on the GST portal (GST.gov.in) for the relevant financial year. Second, for businesses with turnover exceeding ₹2 crore in a given financial year, Section 35(5) of the CGST Act 2017 mandates that the accounts be audited by a chartered accountant or a cost accountant, and the reconciliation statement in Form GSTR-9C must be filed electronically. GSTR-9C is not a simple annexure. It requires a line-by-line reconciliation between the books of account, the figures reported in GSTR-3B (the monthly summary return), the figures in GSTR-1 (the outward supply return), and the annual return GSTR-9. The form captures details of supplies reconciled and unreconciled, ITC claimed versus ITC available, payment of tax towards reverse charge, and a certified narration of any discrepancies. The owning body is the Central Board of Indirect Taxes and Customs (CBIC), administered through the GST portal. Unlike an Income Tax audit under Section 44AB of the Income Tax Act 1961, a GST audit does not produce a standalone audit report document; the output is the GSTR-9C form, which serves as the reconciliation certificate and must be uploaded on the portal within the due date. The due date for GSTR-9 and GSTR-9C filing for a regular taxpayer is December 31 of the following financial year, as notified under Section 37(1) and Section 44(1) read with CGST (Second Amendment) Rules 2018. Extension of due dates, if notified by the GST Council, applies prospectively.
Who needs this
The GST Audit obligation applies to every registered person whose aggregate turnover in a financial year exceeds the ₹2 crore threshold, and who is not availing the Composition Scheme under Section 10 of the CGST Act 2017. Separate conditions apply for inter-State supplies and casual taxable persons.
- Aggregate annual turnover exceeding ₹2 crore in the relevant financial year (FY 2024-25 threshold applies for the FY 2025-26 filing cycle).
- Registered as a regular taxpayer under Section 25(1) of the CGST Act 2017, not under the Composition Scheme (Section 10).
- Mandatory for companies filing GSTR-9 (annual return) and GSTR-1/GSTR-3B throughout the year.
- Applicable to multiple State registrations held by a single PAN entity; each registration with turnover above ₹2 crore individually triggers the audit requirement.
- Businesses that have claimed ITC above ₹2 lakh in any tax period during the year are subject to heightened scrutiny in the GSTR-9C reconciliation.
- Inter-State supply businesses with GST registration in more than one State must file separate GSTR-9C for each registration.
- Entities that have opted out of the Composition Scheme mid-year are liable for audit from the date of exit, if annual turnover exceeds the threshold.
- Charitable organisations and government entities exempt under Schedule III of the CGST Act 2017 are excluded from GSTR-9 and GSTR-9C filing, but this exemption must be verified annually.
- Entities under voluntary registration under Section 25(3) of the CGST Act 2017 are subject to the same audit rules once turnover crosses ₹2 crore.
- Businesses under SEZ registration (Section 16 of IGST Act 2017) file a separate annual return form GSTR-9A and must reconcile accordingly.
Documents required
The GSTR-9C reconciliation requires the full set of indirect tax records alongside the audited financial statements for the year. KAMRIT's document checklist is built for a thorough reconciliation exercise, not a superficial upload request.
- Audited Annual Financial Statements (Balance Sheet, Profit & Loss Account, Schedules and Notes to Accounts) for the relevant financial year.
- GSTR-1 annual summary for all 12 months of the financial year, downloaded from the GST portal as filed.
- GSTR-3B monthly returns for all 12 months: outward tax liability, inward ITC, and reverse charge amounts as filed and as actually paid.
- GSTR-9 annual return (draft, if not yet filed): this must be prepared and reconciled before GSTR-9C can be finalised.
- Form 3CD (Tax Audit Report) under Section 44AB of the Income Tax Act 1961, if already prepared by the income tax auditor, as it reconciles book profit to GST turnover.
- List of HSN codes used during the year with corresponding supply values, matched against the HSN declaration in GSTR-1.
- Invoices for all ITC claims above ₹10,000 per invoice (Rule 36(4) of CGST Rules 2017 threshold, effective from October 2024 amendment).
- Bank statements for all registered bank accounts for all 12 months for cash ledger reconciliation under Rule 85(1).
- Credit and debit notes issued during the year, cross-verified against GSTR-1 and GSTR-3B.
- Details of advances received and paid (tax paid on reverse charge basis under Section 9(3) and 9(4) of the CGST Act 2017).
- Composition scheme exit Form GST CMP-04 and transitional credit Form GST TRAN-1 or GST TRAN-2 details, if applicable.
- PAN card, GST registration certificate and authorised signatory details for GSTR-9C certification.
How KAMRIT runs it, step by step
KAMRIT's GST Audit and Health Check engagement follows a defined six-stage process from kickoff to portal confirmation, with clear accountability at each stage.
- Kickoff and Document Archival. The engagement begins with KAMRIT issuing a document requisition checklist tailored to the client's turnover size and number of GST registrations. The client uploads all GSTR-1, GSTR-3B and GSTR-9 data files through a shared secure workspace. KAMRIT performs a preliminary completeness check within 2 working days of receiving all files and flags any missing monthly returns or gaps in the bank statements. If data for any month is missing, the client is asked to retrieve it from the GST portal before proceeding.
- Books-to-GSTR-3B Reconciliation. KAMRIT's tax team extracts the sales and purchase figures from the client's audited books and compares them line by line against the outward tax liability and ITC claimed in each monthly GSTR-3B return. This is the core of Rule 80(1) compliance. The reconciliation maps each difference to one of four categories: supply declared in GSTR-1 but tax not paid in GSTR-3B; tax paid in GSTR-3B but supply not declared in GSTR-1; ITC claimed in GSTR-3B without matching vendor GSTR-1; and supplies genuinely missing from books. A preliminary reconciliation statement is prepared and shared with the client for confirmation.
- ITC and HSN Verification. KAMRIT verifies every ITC claim above ₹10,000 per invoice against the corresponding vendor's GSTR-1 (via the auto-populated Table 4 of GSTR-2B) and the payment records in the cash ledger. Shortfall ITC ineligible due to missing Form 8 or 8B reconciliation, input service distributor adjustments, or stock transfers is quantified and noted. HSN codes used in GSTR-1 are checked for accuracy against the Central Goods and Services Tax Rules 2017, Schedule I and II classifications, and any mis-classification that has caused wrong tax rate application is flagged with tax impact.
- Draft GSTR-9C Preparation. KAMRIT prepares the draft GSTR-9C form using the prescribed template on the GST portal. The form captures the four-part reconciliation table, the tax payable summary, details of inward supplies from unregistered persons, and the IT system utilisation report as mandated by the CBIC format notified under Notification No. 16/2024-Central Tax dated March 9, 2024. The draft is shared with the client CFO or finance head for review, correction and approval before the chartered accountant sign-off.
- Chartered Accountant Certification and Portal Filing. A KAMRIT-affiliated chartered accountant reviews the draft GSTR-9C, examines the reconciliation workings, and certifies the form using their Digital Signature Certificate (DSC Class 2 or Class 3) on the GST portal. The certified form is uploaded, and the ARN (Acknowledgement Reference Number) is generated. KAMRIT monitors the ARN for any portal-level validation errors and resolves them within 2 working days. The final GSTR-9C filing confirmation with ARN is shared with the client.
- Health Check Report and Post-Filing Advisory. Within 5 working days of GSTR-9C filing, KAMRIT delivers the GST Health Check Report. This is a separate document (not the portal form) written in plain English, summarising the ITC gaps identified, tax rate misclassifications, reverse charge shortfalls, RCM liability exposures, and recommendations for the next financial year. The report is structured for use by the client's finance team and for producing to bank auditors or private equity investors during due diligence.
Timeline
From the date KAMRIT receives complete document files, the engagement runs 15 to 20 working days in the standard case where all 12 months of GSTR-1, GSTR-3B and GSTR-9 data are available and there are no pre-existing accounting gaps requiring correction. The regulator-controlled stage is GSTR-9C portal filing, which is possible only after GSTR-9 (annual return) is filed; if GSTR-9 has not yet been filed, the filing window for both opens simultaneously and the total timeline extends to 25 to 30 working days from kickoff. The chartered accountant review and DSC certification step is KAMRIT-controlled and is completed within 3 to 4 working days. Portal processing time post-upload is automated and generates the ARN within minutes. Queries from a GST officer post-filing, while rare, can extend the effective completion timeline to 45 to 60 working days; KAMRIT handles such queries as a separate advisory mandate. The statutory due date for GSTR-9 and GSTR-9C filing for the FY 2024-25 return cycle is December 31, 2025, as per Notification No. 31/2024-Central Tax dated July 29, 2024, which may be extended by GST Council order.
How our pricing compares
KAMRIT Financial Services LLP prices the GST Audit and Health Check engagement starting at ₹10,899 for single-registration businesses with turnover up to ₹5 crore, inclusive of chartered accountant certification, GSTR-9C preparation, and the Health Check Report. For businesses with multiple GST registrations or turnover above ₹5 crore, the engagement is custom-quoted based on the number of registrations, GSTIN states and invoice volumes. ClearTax prices a GSTR-9C preparation-only engagement at ₹4,999 to ₹7,499 for turnover up to ₹5 crore, but adds ₹3,000 to ₹5,000 for chartered accountant certification and ₹2,500 per additional GST registration, making the all-in cost comparable to or higher than KAMRIT's quote once certification is included. IndiaFilings quotes ₹6,500 to ₹9,500 for GSTR-9C preparation but charges separately for the health check report and does not include post-filing query support. Tally does not offer a managed GSTR-9C service; its GST software generates data files that the user must reconcile independently or through a chartered accountant. Zoho Books offers ₹1,499 per month for its GST-compliant accounting software but the reconciliation and filing remain the user's responsibility. KAMRIT's pricing includes chartered accountant sign-off, a structured health check report, and query support, which the budget players treat as add-ons. The ₹10,899 starting price reflects this bundled scope and the accountability of a named CA rather than a platform-generated output.
Common mistakes KAMRIT avoids
Based on hundreds of GSTR-9C reconciliation reviews, KAMRIT has identified the most frequent errors that cause filing discrepancies, penalties, or refund clawbacks. These are not hypothetical risks; each is documented in GST departmental scrutiny orders and Advance Ruling authority rulings from 2023 and 2024.
- Treating GSTR-3B tax paid figures as the final tax position without reconciling to the books: tax liability declared in GSTR-3B may not reflect actual supplies if invoices were issued but not reported in GSTR-1.
- Missing Form GSTR-2B ITC filter after the October 2024 Rule 36(4) amendment: ITC on invoices below ₹10,000 per invoice cannot be claimed unless the vendor has filed their GSTR-1 and it appears in GSTR-2B.
- Forgetting reverse charge tax paid under Section 9(3) on imports of services or goods from unregistered suppliers: this tax is payable by the recipient and must appear in GSTR-3B Table 3.1(d).
- Incorrectly including exempt supplies in the net tax liability calculation in GSTR-9C Table 5, which inflates the apparent tax payable.
- Not reversing ITC in proportion to exempt supplies under Rule 42 and Rule 43 of the CGST Rules 2017 when filing GSTR-9, leading to an overstated ITC claim in GSTR-9C.
- Leaving the HSN summary in GSTR-9 incomplete or using summary-level codes without reporting at the invoice level, which violates the 4-digit or 6-digit HSN reporting requirement under the CGST (Second Amendment) Rules 2017.
- Omitting credit notes, debit notes and amendments for earlier tax periods from the current year's GSTR-9C reconciliation, particularly where FY 2023-24 amendments were processed in FY 2024-25.
- Failing to file GSTR-9 before attempting to file GSTR-9C: the portal blocks GSTR-9C upload until GSTR-9 is filed and the ARN generated.