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GSTR-9C – Frequently Asked Questions (FAQs)

By Annapoorna


Updated on: Jan 12th, 2022


11 min read

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GSTR-9C is a reconciliation statement between the annual GST return in Form GSTR-9 and the audited financial statements of a taxpayer. It is prepared by a Chartered Accountant/Cost Accountant and later filed by the taxpayer. The reconciliation statement is to ensure the correct self-assessment of tax by a taxpayer. 

Latest Updates

5th July 2022
The CBIC has exempted GST-registered taxpayers with annual aggregate turnover up to Rs.2 crore in FY 21-22 from filing Form GSTR-9.

29th December 2021
The due date to file GSTR-9 & self-certified GSTR-9C for the FY 2020-21 has been extended up to 28th February 2022.

31st July 2021
The CBIC has exempted GST-registered taxpayers with annual aggregate turnover up to Rs.2 crore in FY 20-21 from filing Form GSTR-9.

30th July 2021
The CBIC has notified changes to Sections 35(5) and 44 of the CGST Act. The requirement to get a GST audit and certification done by a CA/CMA now stands removed. Taxpayers with a turnover exceeding Rs.5 crore in the previous financial year are required to file Form GSTR-9C on a self-certification basis. This change is applicable from FY 20-21 onwards. Further, Form GSTR-9C will be modified to support self-certification by the taxpayer.

28th May 2021
As per 43rd GST Council meeting outcome, GSTR-9 shall continue to be optional for taxpayers with turnover up to Rs.2 crore, whereas GSTR-9C can be self-certified by taxpayers with turnover less than or equal to Rs.5 crore from FY 2020-21 onwards.

9th March 2021
The Form GSTR-9A has been disabled from FY 2019-20 onwards for composition taxpayers due to the introduction of GSTR-4 (Annual return). However, the GSTR-9A is optional and can be filed for FY 2017-18 and FY 2018-19.

28th February 2021
The due date to file GSTR-9 & GSTR-9C for the FY 2019-20 has been further extended up to 31st March 2021.

Here are some of the frequently asked questions taxpayers have concerning form GSTR-9C

1. What are the system prerequisites for filing GSTR-9C? 

Below are the system prerequisites for filing Form GSTR-9C: -Windows Operating System should be of version 7 and above -Microsoft Excel should be of 2007 version and above -Internet Explorer to be 10+ -Java should be 1.6 or above -Use the latest offline utility of the Form 

2. What is the time limit to file GSTR-9C and should Form GSTR-9 and Form GSTR-9C be filed separately? 

As per Section 44(2), GSTR-9C should be filed along with the Annual Return GSTR-9. Also, as per Section 44(1), the due date to file Annual Return is on or before 31st December following the end of the financial year for which the return is prepared. Thus, it can be inferred that the due date of filing GSTR-9C is on or before 31st December following the end of the financial year for which the return is prepared. 

3. What are the documents to be enclosed with Form GSTR-9C? 

The following documents are required to be enclosed along with Form GSTR-9C: A copy of the audited financial statements as per Section 35(5) A copy of the audit report where the audit of the entity is carried out by another person under a statute other than the GST Act. 

4. What are the steps for creating a JSON file of Form GSTR-9C? 

Here is a detailed guide to preparing Form GSTR-9C and generating the JSON file using the offline tool. 

5. Can GSTR-9C be revised? 

Currently, there is no provision to revise Form GSTR-9C. Hence, taxpayers are requested to take the utmost care when reporting details in Form GSTR-9C and filing the same. 

6. Can an internal auditor of an entity certify Form GSTR-9C? 

No, as per instructions issued by the ICAI, an internal auditor cannot certify Form GSTR-9C. 

7. Should Form GSTR-9C be filed for state-wise for every registration under the same PAN? 

Yes, Form GSTR-9C should be filed for every registration in each state. Once the PAN-based aggregate turnover exceeds Rs.2 crore, every registered GSTIN having the same PAN is required to get its accounts audited and file Form GSTR-9C. 

8. Should a CA be registered as a GST practitioner for certifying Form GSTR-9C? 

The GST Act does not vest a GST practitioner with the power to audit under section 35(5). It is granted only to a Chartered Accountant or Cost Accountant. Thus, to certify Form GSTR-9C, a CA need not be registered as a GST Practitioner. 

9. How should an auditor provide his Membership Number? 

Auditors prefixing ‘0’ in their membership number should refrain from doing so. If the membership number is ‘020’, then an auditor should enter ‘20’ on the aforesaid part in the membership number field & not ‘020’. 

10. Can GSTR-9C be filed without filing Annual GST Return (GSTR-9)? 

No, GSTR-9C can be filed only after filing GSTR-9. 

11. Which fields are auto-populated from GSTR-9 in Form GSTR-9C? 

Below are the fields which will be auto-populated: 

  • The turnover details as per GSTR-9
  • Liability as per GSTR-9
  • Total tax paid as mentioned GSTR-9
  • Input Tax Credit availed in GSTR-9
12. Does aggregate turnover include stock transfers/cross charges between branches located at different states? 

As per Section 2(6) of the CGST/SGST Act, the term aggregate turnover includes inter-state supplies of persons under the same PAN. Thus, a stock transfer from a branch located in one state to the one located in another state will be included in the turnover of the branch supplying goods/services. 

13. Does aggregate turnover include stock transfers/cross charges between branches located in the same state to determine the threshold limits? 

Branches having the same GSTIN: If both the branches have the same GSTIN, then such stock transfers will not be included in aggregate turnover for determining the threshold limit. 
Branches having different GSTIN: If both the branches have different GSTIN’s, then such stock transfers will be included in aggregate turnover for determining the threshold limit. 

14. Is the supply of alcohol for human consumption included in determining the threshold limit of Rs. 2 crores by a registered person? 

The term aggregate turnover includes exempt turnover. As per CGST Act, exempt turnover means supply of any goods or services or both which attracts nil rate of tax or which may be wholly exempt from tax under section 11, or under section 6 of the Integrated Goods and Services Tax Act and includes non-taxable supply. 

Non-taxable supply is a supply of goods or services which is not chargeable to tax under either the CGST Act or the IGST Act. Section 9(1) of CGST/ SGST Act and Section 7(1) and 5(1) of UTGST and IGST Act specifically excludes alcoholic liquor for human consumption from the levy/charge of GST. Thus, on a combined reading of all the sections it can be inferred that alcoholic liquor for human consumption falls under exempt turnover and as exempt turnover is part of the aggregate turnover, the same should be included in computing the threshold limit of Rs.2 crores. 

15. Does a registered person exclusively deal in exempted supplies exceeding Rs.2 crores, required to file GSTR-9C? 

Yes, because the definition of aggregate turnover includes exempted supplies. 

16. What are the contents of Form GSTR-9C? 

These are the contents of Form GSTR-9C. 

17. What are the late fees for failure in submitting Annual Return and not getting the accounts audited? 

If a taxpayer fails to file both Annual Return and Form GSTR-9C, then he is liable to a fee of Rs.200/- per day during which the default continues (Rs. 100 under CGST law + Rs. 100/- under State / Union Territory GST law) *Capped to a maximum amount of .50% (0.25% under the CGST Law + 0.25% under the SGST / UTGST Law) of turnover in the State/UT. These provisions apply to the filing of GSTR-9; however, no specific provisions apply to GSTR-9C, and hence the filing of GSTR-9 and non-filing of GSTR-9C could be subject to a general penalty of Rs 25,000. 

18. Can the late fee be waived off in genuine cases? 

The Government may do so by way of issue of notification specifying the circumstances but, no such notification has been issued yet. 

19. Which adjustments are to be included/excluded from Table 5C of Form GSTR-9C?

Advances received can be for various purposes. Thus, only the ones on which GST is liable should be considered for the adjustment. Include:

Advances received on services for which the supply has not been made as on 31st March 2021Revenue is not recognized in the books but offered to tax for GST.
Advances received for Goods before 15th Nov 2020 and the supply of goods not complete as on 31st March 2021Revenue is not recognized in the books but offered to tax for GST.


Advance received for exempted services as on 31st March 2021GST is not applicable
Advance received for Goods after 15th Nov 2020GST is not applicable
Financial Advances received which are not adjustable against any servicesNOT a GST Transaction
20. Which details are to be provided in table 5B of Form GSTR-9C? 

Table 5B requires reporting of addition to unbilled revenue at the beginning of the Financial Year. Thus, in simple words, this clause requires reporting of any unbilled revenue, which was recorded in the books of the previous financial year, but the invoice was issued in the current year under the GST law. 

21. Should a taxable person disclose details of notice pay recovery from employees in GSTR-9C? If yes, where should it be reported? 

If the notice pay recovered from employees is considered a taxable supply, but the same is not disclosed as an income in the Profit and Loss account, then it should be reported under Sl.No.5O of GSTR-9C. 

22. Where should the ineligible ITC identified by an auditor which are claimed as eligible by the dealer in GSTR 3B and in Form GSTR 9 be reported in Form GSTR 9C? 

Total ITC availed by the dealer- This is reported in column 3 Part IV of Sl.14 of Form GSTR 9C. Eligible ITC as determined by the auditor- This is reported in column 4 Part IV of Sl.14 of Form GSTR 9C. Thus, the difference between the two is ineligible ITC. The auditor should disclose such ineligible ITC in the Certificate issued by him. 

23. Does the submission of the Form GSTR 9C lead to the understanding that the Commissioner or any officer authorised by him will not undertake an audit under Section 65 of the CGST Act?

No, there are two separate provisions for Departmental Audit and the one done by CA. Section 65 deals with departmental audit, whereas section 35(5) is for Audit to be performed by CA. Audit under section 35(5) is required when aggregate turnover is greater than Rs.2 crores; on the other hand, there is no such condition for audit under section 65. Thus, submission of Form GSTR 9C does not restrict the right of the department to conduct an audit.

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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


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