Complete GST lifecycle on one platform Complete GST lifecycle on one platform
Hyper-automation Hyper-automation
Smart reports & recon Smart reports & recon
Accurate filing Accurate filing

Changes in GSTR-9C for FY 2020-21

By Annapoorna


Updated on: Jan 19th, 2024


10 min read

GSTR-9C is an annual GST reconciliation statement that underwent a major change in 2021. The Form GSTR-9C was earlier applicable to businesses with more than Rs.2 crore as annual turnover in a particular financial year but now applicable of turnover exceeds Rs.5 crore. 

Earlier, it required the audit of books and records of that year by a chartered accountant or a certified management accountant and their certification. These requirements are removed from the financial year 2020-21 onwards. Instead, Form GSTR-9C requires it to be self-certified by the businesses themselves. 

This article provides complete details about the amendment of the provisions of the CGST Act, the format and the corresponding rules governing Form GSTR-9C.

Applicability and format of GSTR-9C before the amendment

Certain businesses had to get their books, represented by the annual financial statements, audited under Section 35(5) of the CGST Act. 

After the conclusion of the GST audit by CA/CMA, the auditor had to sort out any deviations with the management, prepare a reconciliation statement between the audited financial statements and Form GSTR-9 (GST annual returns) filed by the business for a particular financial year. 

The form was known as GSTR-9C provided by Section 44 of the CGST Act, read with CGST Rule 80, and this form had to be certified by the same auditor or a CA/CMA eligible to do so. It had to be prepared for every GSTIN registered under a particular PAN. Once the certification was complete, the business had to file both Form GSTR-9 and Form GSTR-9C on the GST portal on or before the due date of 31st December of the year following that financial year.

The taxpayers could pay any additional liability reported in this form through Form DRC-03. They had to select ― ’Reconciliation Statement’ from the drop-down provided in Form DRC-03 and pay towards such liability only through the electronic cash ledger.

The GST department later considers the information reported in Form GSTR-9C to check for significant discrepancies in the taxpayer’s reporting and compliance. In turn, if it finds any such discrepancy that the taxpayer does not resolve, it can issue notice to the taxpayer.

The format of the erstwhile Form GSTR-9C was divided into two parts. Part-A contained the reconciliation statement with the mention of any differences. Part-B contained the certification by the auditor or CA/CMA.

Part-A was further divided into five parts as follows:

Part No.Particulars
Part-IBasic details such as GSTIN, FY, Trade name and legal name, and any requirement of audit under any other law.
Part-IIReconciliation between the turnover derived from the audited annual financial statement for a particular GSTIN and the turnover mentioned in Form GSTR-9 (GST annual returns).
Part-IIIReconciliation and differences, if any, between the GST-rate wise tax liability and payment as reported in Form GSTR-9 and derived from the audited financial statements for a particular GSTIN. 
Part-IVReconciliation and differences, if any, between the input tax credit availed and used as reported in Form GSTR-9 and derived from the audited financial statements for a particular GSTIN.
Part-VAuditor’s recommendation regarding any additional unreconciled liabilities.

Part-B had two varieties for use. The auditor could use the first type or format for certifying the Form GSTR-9C himself. The second type or format could be used by a CA/CMA who did not perform the audit but certifies the Form GSTR-9C based on the auditor’s observations.

Changes introduced by the Union Budget 2021 and notifications

The Union Budget 2021 introduced two key changes in Sections 35 and 44 of the CGST Act. The government has removed Section 35(5) of the CGST Act. Further, Section 44 of the CGST Act stands amended. The changes in the Act were approved with the passing of the Finance Act, 2021.

Following are the changes in the CGST Act-

  • The need for a GST audit by CA/CMA stands removed for FY 2020-21 and any later financial years.
  • Every applicable taxpayer must submit a self-certified reconciliation statement by reconciling values between the audited financial statements and the annual returns.
  • Some taxpayers may be exempted from complying with the annual return and reconciliation statement requirement through the CBIC notification.
  • Section 44 shall not apply to any central government or state government departments already subject to audit by the Comptroller and Auditor-General of India (CAG).

The GST Council reaffirmed these changes at the 43rd GST Council meeting held on 28th May 2021. The CBIC notified these changes on 30th July 2021 vide Central Tax notifications 29/2021 and 30/2021. It notified the applicability of Sections 110 and 111 of the Finance Act, 2021 that contained these amendments. Further, Rule 80(3) and Part-B of the CGST Rules have been amended to specify the threshold limit for applicability and bring changes to the format. 

Accordingly, Form GSTR-9C applies to a taxpayer if the annual aggregate turnover limit for the relevant financial year is more than Rs.5 crore. The format of Form GSTR-9C has been modified to include FY 2020-21 and to support self-certification.

Applicability of Form GSTR-9C from FY 2020-21 onwards

Form GSTR-9C continues to be exempted for input service distributors, taxpayers subject to TDS and TCS provisions, casual taxable persons and non-resident taxable persons. In addition to these, government departments and taxpayers with a total turnover less than or equal to Rs.5 crore are added to the exemption category.

Accordingly, Form GSTR-9C becomes applicable to taxpayers with an annual aggregate turnover for the relevant financial year being more than Rs.5 crore. These taxpayers are required to self certify or carry out a voluntary reconciliation statement without the need for audit and file it with the tax authority on or before 31st December of the year following the relevant financial year.

The following table summarises the threshold applicability of both annual returns and the reconciliation statement for FY 2020-21.

Name of the FormApplicability- AATO* limit for FY 2020-21The due date for FY 2020-21
GSTR-9> Rs.2 crore31st December 2021
GSTR-9C> Rs.5 crore

*Annual aggregate turnover during FY 2020-21.

Summarised table of changes to Form GSTR-9C

(Changes applicable for FY 2020-21 and onwards)

Changes in Part-A: Reconciliation statement is as follows:

Reference to part and/or table no.Particulars Changes made
Part-II – Tables 5B to 5NReconciliation of the annual turnover as per the audited annual financial statement with the turnover as declared in Form GSTR-9These tables are optional while filing GSTR-9C for FY 2020-21. If there are any adjustments, those can be done in Table 5O. Rest of fields in Table 5 are mandatory.
Part-III and Table no. 9Reconciliation of GST rate-wise liability and the amount payable A new row is inserted below ‘K’ -0.10% to now have ‘K-1’ for other GST rates not listed above it.
Part-III and Table no. 11Any additional amount to be paid but not paid (on account of the reasons specified under Tables 6,8 and 10)A new row ‘others’ is inserted below 0.10% to now have other GST rates not listed above it.
Part-IV- Tables 12B, 12C, and 14Reconciliation of Input Tax Credit (ITC)These tables are optional while filing GSTR-9C for FY 2020-21.

Auditor’s recommendation on any additional Liability due to non-reconciliation
Heading changed to “Additional Liability due to non-reconciliation”A new row ‘others’ is inserted below 0.10% to now have other GST rates not listed above it.
Verification Verification of the registered person

Replaced by the following lines:I hereby solemnly affirm and declare that the information given herein above is true and correct, and nothing has been concealed therefrom. I am uploading the self-certified reconciliation statement in Form GSTR-9C. As applicable, I am also uploading other statements, including financial statements, profit and loss account and balance sheet, etc.
Instruction -serial no. 7Part V – Additional Liability due to non-reconciliationThe wordings of the instruction are revised to remove references to the auditor and their recommendations, as follows:Part-V consists of the additional liability to be discharged by the taxpayer due to non-reconciliation of turnover or non-reconciliation of the input tax credit. Any refund that has been mistakenly considered and paid back to the government must also be declared in this table. Lastly, any other pending demand to be settled by the taxpayer has to be declared in this Table.

Part-B – Certification has been entirely removed 

CFO or Finance Head’s responsibility towards self-certified GSTR-9C

No doubt that with the removal of the GST audit and certification by CA/CMA, compliance seems to have been simplified for taxpayers. On the flip side, the Finance Head’s of the taxpayer business have added responsibility on their shoulders to report the figures in Forms GSTR-9 and GSTR-9C accurately. 

Every CFO or Finance Head of the applicable company must first ensure that their teams are aligned with the changes in the format of GSTR-9 and GSTR-9C. They should arrange for awareness sessions for their teams to understand the implications of removing the requirement of GST audit and certification by a CA/CMA.

The government does not intend to reduce its verification measures with the removal of the GST audit. It may even increase the scrutiny procedures and impose penalties where it identifies any non-compliance or lapse in reporting. Businesses must notify any unreconciled figures as it is in Form GSTR-9C, without any omissions. Companies may refer to the opinions and observations made by the statutory auditors regarding GST compliance while preparing GSTR-9C.

There is always a fear of GST registrations getting suspended for significant discrepancies in data between GST returns – GSTR-1 versus GSTR-3B versus books and GSTR-3B versus GSTR-2A versus books. The GST law added this ground for the suspension of GST registration with effect from January 2021. 

Hence, finance heads must have dedicated team members to perform these reconciliations before the deadline prescribed by the law for adjustments and corrections to GST data reported for a particular financial year. The deadline is due date for filing GSTR-1 and GSTR-3B of October of the year following the relevant financial year (The law prescribes deadline of 30th November of following year or annual return filing date whichever is earlier). 

These actions allow the business to prepare and report accurate GST annual returns and reconciliation statements with lower chances of any GST demand notices. In turn, they can avoid paying any tax dues through Form DRC-03 later on, during or after filing GSTR-9 and GSTR-9C.

CFOs must set up robust systems in their organisations for annual GST reconciliation at the PAN-India level. Even though reporting is at GSTIN-level, the finance leaders must ensure data consistency in annual returns compared to the income tax returns, which can be achieved through automation and tech-enabled systems.

Clear GST software offers the ultimate solution to tackle your enterprise’s annual GST compliance, such as the yearly GST reconciliation due with the filing of October returns and the preparation and filing of GSTR-9 and GSTR-9C. Sign up and begin your GST-compliant journey with ease!

About the Author

I preach the words, “Learning never exhausts the mind.” An aspiring CA and a passionate content writer having 4+ years of hands-on experience in deciphering jargon in Indian GST, Income Tax, off late also into the much larger Indian finance ecosystem, I love curating content in various forms to the interest of tax professionals, and enterprises, both big and small. While not writing, you can catch me singing Shāstriya Sangeetha and tuning my violin ;). Read more

Public Discussion

Get involved!

Share your thoughts!


Quick Summary

Changes to Form GSTR-9C include self-certification for businesses with turnover above Rs.5 crore, removed audit by CA/CMA requirement, and format modifications. Taxpayers must ensure accurate reporting to avoid penalties and suspension of GST registrations for discrepancies. Businesses can leverage tech-enabled systems and clear GST software for compliance. Union Budget 2021 introduced key changes in the CGST Act affecting Form GSTR-9C.

Was this summary helpful?

Clear offers taxation & financial solutions to individuals, businesses, organizations & chartered accountants in India. Clear serves 1.5+ Million happy customers, 20000+ CAs & tax experts & 10000+ businesses across India.

Efiling Income Tax Returns(ITR) is made easy with Clear platform. Just upload your form 16, claim your deductions and get your acknowledgment number online. You can efile income tax return on your income from salary, house property, capital gains, business & profession and income from other sources. Further you can also file TDS returns, generate Form-16, use our Tax Calculator software, claim HRA, check refund status and generate rent receipts for Income Tax Filing.

CAs, experts and businesses can get GST ready with Clear GST software & certification course. Our GST Software helps CAs, tax experts & business to manage returns & invoices in an easy manner. Our Goods & Services Tax course includes tutorial videos, guides and expert assistance to help you in mastering Goods and Services Tax. Clear can also help you in getting your business registered for Goods & Services Tax Law.

Save taxes with Clear by investing in tax saving mutual funds (ELSS) online. Our experts suggest the best funds and you can get high returns by investing directly or through SIP. Download Black by ClearTax App to file returns from your mobile phone.

Cleartax is a product by Defmacro Software Pvt. Ltd.

Company PolicyTerms of use


ISO 27001

Data Center


SSL Certified Site

128-bit encryption