What is the turnover limit for GSTR-9C filing?

The GSTR-9C filing threshold is aggregate turnover above INR 5 crore in a financial year (CBIC Notification No. 29/2021 dated 30 July 2021, effective from FY 2020-21). This is computed on an all-India PAN basis - all GSTINs under the same PAN are clubbed. GSTR-9 (annual return) is mandatory for turnover above INR 2 crore; optional below INR 2 crore per Notification 15/2025 for FY 2024-25.

Is CA certification required for GSTR-9C?

No. From FY 2020-21 onwards, GSTR-9C is self-certified by the taxpayer. The Finance Act, 2021 amended Section 35(5) of the CGST Act to remove the mandatory CA/CMA certification requirement. Previously (up to FY 2019-20), businesses with turnover above INR 2 crore required CA or Cost Accountant certification. However, professional representation remains critical for departmental audits.

What happens during a Section 65 departmental GST audit?

Under Section 65, the Commissioner issues Form GST ADT-01 at least 15 working days before audit commencement. The audit covers GST records for up to 5 financial years (Rule 101 CGST Rules). It must be completed within 3 months, extendable by 6 months. Within 30 days of conclusion, the officer communicates findings in Form GST ADT-02. If tax is found short-paid or ITC wrongly availed, proceedings under Section 73 or 74 may be initiated.

What is the penalty for not filing GSTR-9C?

There is no specific penalty prescribed for GSTR-9C non-filing. The general penalty under Section 125 of CGST Act may apply - up to INR 25,000 for CGST and INR 25,000 for SGST (INR 50,000 total). Additionally, GSTR-9C late filing attracts a late fee of INR 200 per day (INR 100 CGST + INR 100 SGST), capped at 0.5% of the taxpayer's turnover in the state.

What documents should I prepare before a GST audit?

Key documents include: all GST returns (GSTR-1, GSTR-3B, GSTR-9), GSTR-2B auto-drafted statements, purchase and sales registers, ITC ledgers, audited financial statements, bank statements, stock records, e-way bill logs, and any prior GST notices or orders. For departmental audits, trial balance and cost audit/income tax audit reports may also be required under Section 65(5) of CGST Act.

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GST Audit Services in India

Q: What is GST audit and who needs to undergo it in India?

GST audit is the examination of a registered taxpayer's records, returns, and documents under the CGST Act, 2017 to verify correctness of turnover, taxes paid, ITC availed, and refunds claimed [Section 2(13)]. All businesses with aggregate turnover above INR 5 crore must file GSTR-9C (self-certified reconciliation statement) by 31 December following the financial year. Any registered person may also face a departmental audit under Section 65 regardless of turnover.

Q: Kya GST audit sirf badi companies ke liye hoti hai?

Nahi. GSTR-9C filing turnover above INR 5 crore wale businesses ke liye mandatory hai. Lekin Section 65 ke under departmental audit kisi bhi registered taxpayer par ho sakta hai - chahe turnover chhota ho ya bada. Department ise risk-based parameters par select karta hai, jaise ITC mismatch, return filing irregularities, ya industry-specific risks. Quick Answers What is GST audit? Examination of a taxpayer's GST records, returns, and documents to verify accuracy of turnover, ITC availed, taxes paid, and refunds claimed under the CGST Act, 2017. Who files GSTR-9C? All GST-registered regular taxpayers with aggregate annual turnover exceeding INR 5 crore must self-certify and file GSTR-9C, per CBIC Notification 29/2021. Is GSTR-9C mandatory? Yes, for turnover above INR 5 crore. Must be filed by 31 December following the relevant FY along with GSTR-9 and audited accounts. What is Section 65 audit? Section 65 of CGST Act authorizes the Commissioner to audit any registered taxpayer. ADT-01 notice given at least 15 working days in advance; audit completes in 3-9 months. GST audit penalty amount? General penalty under Section 125 is up to INR 25,000 (CGST) and INR 25,000 (SGST). Late filing of GSTR-9C attracts INR 200/day capped at 0.5% of turnover.

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GSTR-9C Self-Certified Reconciliation: For businesses with aggregate turnover above INR 5 crore (per CGST Act, Section 44 read with CBIC Notification 29/2021) - end-to-end preparation and filing.

Section 65 Departmental Audit Representation: Full support from ADT-01 notice receipt to final ADT-02 findings - document compilation, officer coordination, reply drafting, and demand prevention.

ITC Verification and Reconciliation: GSTR-1 vs GSTR-3B vs GSTR-2B reconciliation, blocked credit identification under Section 17(5), and HSN-SAC classification review.

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Patron Accounting handled our GSTR-9C for three GSTINs seamlessly. Their reconciliation report caught INR 1.2 lakh in excess ITC we had missed - saving us from a potential demand.

Anil Kumar

CFO, Manufacturing, Pune

★★★★★

2 months ago

“

When we received an ADT-01 notice for Section 65 audit, Patron's team stepped in within 24 hours and managed the entire process. Zero demand raised at conclusion.

Priya Menon

Director, IT Services, Bangalore

★★★★★

3 months ago

“

Professional, thorough, and always reachable. Their GST compliance health check identified issues with our RCM calculations that we had been getting wrong for 2 years.

Rahul Gupta

Founder, E-commerce, Mumbai

★★★★★

1 month ago

“

Multiple GSTINs across 4 states - Patron prepared all GSTR-9C forms consistently and on time. Their ITC reconciliation was the most thorough we have seen.

Sneha Deshmukh

Finance Manager, FMCG, Delhi

★★★★★

4 months ago

“

Patron's CA team helped us file DRC-03 for a short-payment we discovered during GSTR-9C preparation. Saved us from interest under Section 50. Highly recommended.

Vijay Joshi

Proprietor, Trading, Pune

★★★★★

2 months ago

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Overview What Is It Applicability Our Services 7-Step Process Documents Challenges Fees Timeline Benefits DIY vs CA FAQs

GST Audit Services in India - Complete Guide 2026

📌 TL;DR - GST Audit Services at a Glance

GST audit is the systematic examination of a registered taxpayer's records, returns, and financial documents to verify turnover, ITC availed, tax paid, and compliance with the CGST Act, 2017. GSTR-9C is self-certified (not CA-certified) from FY 2020-21 onwards per Finance Act 2021. Mandatory for aggregate turnover above INR 5 crore. Departmental audit under Section 65 can target any taxpayer. Penalty up to INR 25,000 under Section 125. Patron Accounting starting at INR 9,999 (Exl GST and Govt. Charges).

Whether your business is facing a routine GSTR-9C filing, a Section 65 departmental audit notice (Form GST ADT-01), or a Section 66 special audit direction, Patron Accounting's experienced CA team provides end-to-end support - from ITC reconciliation to final filing and post-audit representation.

Parameter	Key Detail
Governing Act	CGST Act, 2017 - Sections 44, 65, 66 read with Rules 80, 101, 102
Who Files GSTR-9C	Businesses with aggregate turnover above INR 5 crore (FY 2020-21 onwards)
GSTR-9 Filing	Mandatory for turnover above INR 2 crore; optional below INR 2 crore (FY 2024-25)
GSTR-9C Due Date	31 December of the following financial year (e.g., 31 Dec 2025 for FY 2024-25)
Departmental Audit (Sec 65)	Commissioner-directed; 15 working days' notice in ADT-01; completed in 3-9 months
Special Audit (Sec 66)	Directed by Asst. Commissioner with Commissioner approval; CA/CMA conducts; 90-180 days
Penalty	General penalty up to INR 25,000 under Section 125 of CGST Act

With evolving compliance requirements - including the shift from CA-certified audit to self-certified GSTR-9C under Finance Act 2021 - businesses need expert support to avoid notices, demands, and penalties. GST audit kya hoti hai aur kaise hoti hai? Patron Accounting ki CA team se sampark karein - GSTR-9C reconciliation se lekar departmental audit representation tak, hum sab handle karte hain.

Content is reviewed quarterly for accuracy.

What is GST Audit?

GST Audit is the examination of records, returns, and documents maintained or furnished by a registered taxpayer under the CGST Act, 2017, to verify the correctness of turnover declared, taxes paid, refunds claimed, and Input Tax Credit availed - as defined under Section 2(13) of the CGST Act, 2017.

Until FY 2019-20, Section 35(5) required businesses with aggregate turnover exceeding INR 2 crore to get accounts audited by a CA/CMA and submit GSTR-9C certified by that professional. From FY 2020-21 onwards, the Finance Act 2021 removed mandatory CA/CMA certification. GSTR-9C is now self-certified by taxpayers with turnover above INR 5 crore (per CBIC Notification No. 29/2021 dated 30 July 2021). However, departmental and special audits by tax authorities continue under Sections 65 and 66.

Key Terms for GST Audit:

GSTR-9: Annual GST return consolidating all monthly/quarterly returns (GSTR-1, GSTR-3B) for a financial year. Mandatory for turnover above INR 2 crore.

GSTR-9C: Annual reconciliation statement (formerly audit form). Self-certified by taxpayer for turnover above INR 5 crore. Reconciles GSTR-9 data with audited financial statements.

Aggregate Turnover: PAN-level, all-India aggregate of all taxable, exempt, and export supplies excluding GST. All GSTINs under the same PAN are clubbed together.

ITC (Input Tax Credit): Tax credit on inward supplies eligible for set-off against output GST liability. Central to audit scrutiny - incorrect claim attracts demand and reversal.

ADT-01: Notice form issued to registered person at least 15 working days before a Section 65 departmental audit.

ADT-02: Final findings form communicated to taxpayer within 30 days of audit conclusion under Section 65(6).

CGST Act GSTR-9C Reconciliation

GST Audit Applicability - Who Needs It?

GSTR-9C (Self-Certified Reconciliation Statement)

Applicable to all regular GST-registered taxpayers with aggregate turnover above INR 5 crore in a financial year
Not applicable to Composition scheme taxpayers, OIDAR service providers, foreign airlines
Due Date: 31 December following the relevant FY (e.g., FY 2024-25 due by 31 December 2025) [Section 44 CGST Act]
Self-certified - CA/CMA certification no longer mandatory from FY 2020-21 onwards

Section 65 - Departmental Audit

Applicable to any GST-registered person - no turnover threshold; selected based on risk parameters
Minimum 15 working days prior notice in Form GST ADT-01 [Section 65(3)]
Scope covers previous 5 years of financial records (Rule 101 CGST Rules)
Must be completed within 3 months, extendable by 6 months [Section 65(4)]

Section 66 - Special Audit

Directed by Assistant Commissioner with prior Commissioner approval to a nominated CA/CMA
Triggered by undervaluation, excess ITC claim, or complexity requiring specialist examination
90 days for completion, extendable to 180 days [Section 66 CGST Act]

Patron Accounting GST Audit Services

Service	What We Do
GSTR-9C Preparation and Filing	End-to-end preparation of the annual reconciliation statement - reconciling GSTR-9 with audited accounts, identifying discrepancies, self-certifying for submission
GSTR-9 Annual Return Filing	Comprehensive preparation consolidating all GSTR-1, GSTR-3B, and GSTR-2B data with HSN-SAC summary and ITC details
ITC Reconciliation and Verification	Detailed reconciliation of ITC in GSTR-3B against GSTR-2B, ineligible ITC identification, reversal computations
Section 65 Departmental Audit Representation	Full support from ADT-01 notice to ADT-02 findings - document compilation, officer coordination, reply drafting
Section 66 Special Audit Assistance	Expert assistance during special audits - record organization, CA/CMA coordination, response to findings
GST Compliance Health Check	Pre-audit review of all GST returns, ITC claims, exemptions, e-way bills, and records to identify issues

Our Process

GST Audit Procedure - 7-Step Process

Our CA team follows a structured 7-step process for every GST audit engagement - from initial assessment to GSTR-9C filing and post-audit support.

Step 1

Initial Assessment and Scope Definition

We review your GST registration, business category, aggregate turnover (all-India PAN basis), and GSTIN details. We determine applicability of GSTR-9C, GSTR-9, and any pending departmental notices.

Applicability confirmed Scope defined

Assessed01

Step 2

Document Collection

We collect all GST returns (GSTR-1, GSTR-3B, GSTR-9), purchase and sales registers, ITC ledgers, stock records, audited financial statements, e-way bill logs, and any prior GST notices.

All returns collected Financial statements received

Collected02

Step 3

ITC and Turnover Reconciliation

We reconcile ITC claimed in GSTR-3B against auto-populated GSTR-2B, identify blocked credits under Section 17(5), and reconcile turnover across GSTR-1, GSTR-3B, and audited accounts.

ITC reconciled Turnover verified

Reconciled03

Step 4

HSN/SAC Classification and Rate Verification

We verify correct HSN/SAC codes on outward and inward supplies, confirm tax rate applied on each supply category, and flag any rate mismatch that could attract demand under Section 73 or 74.

HSN/SAC codes verified Rate mismatches flagged

Classified04

Step 5

Discrepancy Identification and Resolution

All discrepancies between GSTR-9 and audited financials are documented. Where short-payment is found, we compute additional liability and arrange payment via DRC-03 before filing GSTR-9C.

Discrepancies documented DRC-03 payment arranged

Resolved05

Step 6

GSTR-9C Preparation and Self-Certification

We prepare the complete GSTR-9C reconciliation statement as per Section 44 of CGST Act. The statement is prepared per GSTIN and self-certified by the authorized signatory of the taxpayer.

GSTR-9C prepared per GSTIN Self-certified

Prepared06

Step 7

Filing and Post-Filing Support

We file GSTR-9C on the GST portal along with GSTR-9 and audited accounts. We provide post-filing support for queries, scrutiny notices (ASMT-10), and any demand notices arising from the audit.

Filed on GST portal Post-filing support available

Filed07

Legal Verification Gate: All thresholds and timelines cited above are verified against CGST Act, 2017 provisions and current CBIC notifications as of March 2026.

Documents Required for GST Audit

GST Returns

GSTR-1 (monthly/quarterly) for all periods under review
GSTR-3B (monthly/quarterly) for all periods under review
GSTR-9 annual return (if already filed)
GSTR-9C reconciliation statement (if previously filed)
GSTR-2B auto-drafted statements for all months

Financial Records

Audited annual financial statements (Balance Sheet, P&L, Notes to Accounts)
Books of accounts - purchase register, sales register, expense ledgers
Bank statements for the audit period
Trial balance and ledger summaries

GST-Specific Records

ITC register - availed, reversed, and re-availed by month
E-way bill log for supplies above INR 50,000 value [Rule 138 CGST Rules]
Stock register and inventory records
RCM (Reverse Charge Mechanism) liability register
Export invoices, shipping bills, and LUT/bond (if applicable)
HSN/SAC-wise outward supply summary

Common GST Audit Challenges and How We Solve Them

Challenge	Impact	How Patron Accounting Solves It
ITC Mismatch Between GSTR-3B and GSTR-2B	Demand and interest under Section 50 CGST Act	Month-wise reconciliation, eligible/ineligible credit identification, correct reversal structuring to prevent demand
Turnover Reporting Discrepancy	Major audit trigger - differences between GSTR-1, GSTR-3B, and audited financials	Three-way reconciliation, reasons documented (credit notes, advances, cancellations) in Part II of GSTR-9C
Section 65 Departmental Audit Notice	ADT-01 notice - stress and potential demand	Immediate review of scope, document compilation, expert representation to ensure factual findings and minimized demands
Short Payment Discovered Late	Demand under Section 73 (non-fraud) or 74 (fraud)	Voluntary payment via DRC-03 before audit to reduce interest and avoid penalties

GST Audit Fees in India - 2026 Pricing

Fee Component	Amount
Patron Accounting Professional Fees - GSTR-9C (Single GSTIN, Turnover INR 5-10 crore)	Starting from INR 9,999 (Exl GST and Govt. Charges)
GSTR-9C (Single GSTIN, Turnover INR 10-50 crore)	Starting at INR 7,999 per GSTIN
GSTR-9C (Turnover above INR 50 crore)	Custom pricing - contact us
GSTR-9 Annual Return Filing (standalone)	Starting at INR 2,499
GST Compliance Health Check	Starting at INR 3,999
Section 65 Departmental Audit Representation	Starting at INR 9,999 per year under audit
Multiple GSTIN (same PAN)	Discounted bundled pricing available

All fees and charges listed are indicative only and do not constitute a binding offer. Final amounts may vary depending on the volume of work and the complexity involved.

Professional service charges for drafting, filing, and representation are separate from the statutory fees. The exact fee depends on the complexity of the case, disputed amount, and number of hearings required. Contact us for a detailed quote.

Get a free GST Audit consultation - Call +91 945 945 6700 or WhatsApp us. No-obligation assessment.

GST Audit Timeline - How Long Does It Take?

Stage	Estimated Timeline
GSTR-9C (Standard - single GSTIN, clean records)	7-14 working days from document collection
GSTR-9C (Complex - multiple GSTINs, export transactions)	15-25 working days
Section 65 Departmental Audit (ADT-01 to ADT-02)	3 months; extendable by 6 months [Section 65(4) CGST Act]
Section 66 Special Audit (ADT-03 to report)	90 days; extendable by 90 days [Section 66 CGST Act]
GST Compliance Health Check	5-7 working days

Deadline Alert: GSTR-9C for FY 2024-25 is due by 31 December 2025. Late filing attracts INR 200/day (INR 100 CGST + INR 100 SGST), capped at 0.5% of state-wise turnover. Engage early to avoid last-minute rush and errors.

Key Benefits

Why Choose Patron Accounting for GST Audit?

Avoid Costly Demands

Accurate reconciliation prevents short-payment detection during departmental audit, which can trigger demand + 18% interest under Section 50 of CGST Act.

Proactive ITC Optimization

Our team identifies eligible ITC that may have been missed, improving cash flow and reducing GST liability for your business.

Audit-Ready Documentation

Organized records, reconciliation schedules, and workings ensure you are prepared for any tax authority scrutiny at any time.

Expert Representation

Experienced CA team handles Section 65 departmental audits professionally, reducing the risk of adverse findings and inflated demands.

Year-Round Support

Beyond the audit, we help establish systems for monthly reconciliation, on-time filings, and compliance management throughout the year.

Penalty Prevention

Identifying discrepancies before GSTR-9C filing and resolving via DRC-03 voluntary payment eliminates penalty risk under Section 125.

1,000+ GST Audits Completed Across India

"Patron Accounting handled our GSTR-9C for three GSTINs seamlessly. Their reconciliation report caught INR 1.2 lakh in excess ITC we had missed." - CFO, Manufacturing Company, Pune

"When we received an ADT-01 notice, Patron's team stepped in within 24 hours and managed the entire audit. Zero demand raised." - Director, IT Services Company, Bangalore

"Professional, thorough, and always reachable. Their GST health check saved us from a potential penalty." - Founder, E-commerce Business, Mumbai

DIY Filing vs Professional GST Audit Support

Parameter	DIY Filing	Patron Accounting
ITC Reconciliation Accuracy	Manual, error-prone	Multi-layer verification using reconciliation tools
GSTR-9C Preparation Time	2-4 weeks (internal team)	7-14 working days
Section 65 Audit Handling	Internal staff, no legal expertise	Experienced CA representation from notice to closure
Risk of Demand/Penalty	High - errors often discovered post-filing	Low - discrepancies resolved before filing
Cost	Staff time + opportunity cost	Starting at INR 9,999 - clear ROI
Post-Audit Support	Limited	Available year-round for follow-up notices

Related GST and Audit Services

GST Returns Filing - accurate monthly/quarterly GSTR-1 and GSTR-3B filing to minimize reconciliation issues at audit time
GST Registration - new business GST registration, amendment, and cancellation
GST Notice Response - expert handling of ASMT-10, SCN, and demand notices from GST department
Tax Audit Service - Income Tax Act audit under Section 44AB for businesses above turnover threshold
Statutory Audit Service - Companies Act, 2013 audit for private limited companies and LLPs

Legal Framework for GST Audit in India

Legal Provision	Relevance to GST Audit
Section 2(13) CGST Act, 2017	Definition of GST Audit - examination of records, returns, and documents to verify compliance.
Section 35(5) CGST Act (amended)	Mandatory CA/CMA audit removed from FY 2020-21 via Finance Act, 2021. GSTR-9C now self-certified.
Section 44 CGST Act	Annual return and reconciliation. GSTR-9C to be filed with GSTR-9 for turnover above INR 5 crore.
Section 65 CGST Act	Departmental audit by tax authorities. 15 working days' notice. 3-month completion, extendable by 6 months. Source: CBIC
Section 66 CGST Act	Special audit directed by Asst. Commissioner with Commissioner approval. CA/CMA nominated. 90-180 days.
Section 73 CGST Act	Demand for tax not paid/short paid (non-fraud). 3-year limitation. 10% penalty or INR 10,000.
Section 74 CGST Act	Demand involving fraud/wilful misstatement/suppression. 5-year limitation. 100% penalty.
Section 125 CGST Act	General penalty - INR 25,000 maximum (CGST/SGST) for non-compliance where no specific penalty prescribed.
CBIC Notification 29/2021 - CT	Effective 1 August 2021 - Section 35(5) CA/CMA certification removed. GSTR-9C self-certification for turnover above INR 5 crore. Source: GST Portal

Frequently Asked Questions - GST Audit in India

Get answers to common questions about GST audit, GSTR-9C filing, Section 65 departmental audit, penalties, and compliance requirements.

Quick Answers

What is GST audit? Examination of a taxpayer's GST records, returns, and documents to verify accuracy of turnover, ITC availed, taxes paid, and refunds claimed under the CGST Act, 2017.

Who files GSTR-9C? All GST-registered regular taxpayers with aggregate annual turnover exceeding INR 5 crore must self-certify and file GSTR-9C, per CBIC Notification 29/2021.

Is GSTR-9C mandatory? Yes, for turnover above INR 5 crore. Must be filed by 31 December following the relevant FY along with GSTR-9 and audited accounts.

What is Section 65 audit? Section 65 of CGST Act authorizes the Commissioner to audit any registered taxpayer. ADT-01 notice given at least 15 working days in advance; audit completes in 3-9 months.

GST audit penalty amount? General penalty under Section 125 is up to INR 25,000 (CGST) and INR 25,000 (SGST). Late filing of GSTR-9C attracts INR 200/day capped at 0.5% of turnover.

GSTR-9C for FY 2024-25 is Due by 31 December 2025

Late filing attracts INR 200/day (INR 100 CGST + INR 100 SGST), capped at 0.5% of state-wise turnover. Do not miss the deadline.

GSTR-9C due date: 31 December 2025 for FY 2024-25 [Section 44, CGST Act]
Late fee: INR 200 per day, maximum 0.5% of state-wise turnover
Short-payment discovered: Pay via DRC-03 before filing to avoid 18% interest under Section 50
Section 65 notice received: Respond immediately - audit must complete within 3 months of commencement

Start Your GST Audit Engagement Today - Free Consultation

GST audit - whether through mandatory GSTR-9C self-certification, a Section 65 departmental audit, or a Section 66 special audit - is a critical compliance obligation that directly impacts your tax liability, ITC position, and standing with the GST department. An unresolved discrepancy between GSTR-9 and audited accounts can trigger demand notices, interest under Section 50, and penalties under Sections 73, 74, or 125.

Patron Accounting's experienced CA team provides structured, thorough GST audit support - from GSTR-9C preparation and ITC reconciliation to full departmental audit representation. Our offices in Pune, Mumbai, Bangalore, and Delhi serve businesses across India.

Starting at INR 9,999 (Exl GST and Govt. Charges) | GSTR-9C + ITC Reconciliation | Section 65 Representation | Pan-India

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GST Audit Services - Available in Your City

Patron Accounting provides expert GST Audit services including GSTR-9C reconciliation and departmental audit representation across major cities in India.

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Content Created: March 2026 | Last Updated: 20 April 2026 | Next Review: March 2027 | Reviewed By: CA & CS Team, Patron Accounting LLP

This page covers GST Audit Services in India including GSTR-9C reconciliation, Section 65 departmental audit, and Section 66 special audit. Content is reviewed annually. All regulatory references verified against CGST Act provisions and CBIC notifications as of March 2026.

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