GSTR-9C Late Fees Waiver

GSTR-9C is a mandatory GST return for those who are registered under GST and have an aggregate turnover of equal to or more than ₹ 2 Crores. This return is an annual reconciliation statement. Under this return, details of the taxpayer’s annual GST return and their audit financial statement are compared. Failing to file the return attracts late fees, which is ₹200 per day or a maximum of 0.5% of the turnover. In January 2025, the Central Board of Indirect Taxes and Customs (CBIC) announced relaxation in GSTR–9C via Notification No. 8/2025. 

What are the conditions under which GSTR-9C late fees waiver is applicable. For which financial year is it applicable? We will answer these questions in detail through this blog. 

Implications of Not Filing GSTR-9C

In any case, if you fail to file a GSTR–9C return before the deadline, i.e. March 31, 2025, the tax authorities may take decisive actions against you and your organization for not complying with the regulations. The authorities may initiate any of the following proceedings against you: 

Show Cause Notice (SCN)

Initially, the concerned authorities may send you a Show Cause Notice (SCN), providing a strict timeframe to file the pending GSTR-9C return. The Show Cause Notice can be issued under the following circumstances: 

• Section 73 for non-fraudulent discrepancies
• Section 74 for fraudulent activities

Read More: GSTR-9C Filing Process

Penalties 

If you fail to file GSTR-9C in a timely manner, it can attract penalties under Section 125 of the CGST Act, amounting to up to ₹25,000 for non-compliance. 

State GST Penalties: State GST laws authorize state governments to impose additional penalties other than Central GST, leading to doubling the financial burden. 

Late Fees: Filing GSTR-9C late attracts penalties, burdening taxpayer’s financial liabilities. 

GST Audits and Assessments: The GST authorities may initiate an audit trail or assessment proceedings to scrutinize your filings and to find any discrepancies. 

Enhanced Scrutinity: Repeated failure to file GSTR-9C can lead to increased scrutiny on your GST returns, potentially leading to allegations of tax evasion. 

Late Fees Charged on GSTR-9C Filing 

GSTR-9C is an annual GST return that is to be filed after filing GSTR-9C; in case you fail to file, you may have to pay late fees, details of which are as follows:  

Turnover	Late fees (Per day)	Maximum late fees
Up to ₹2 Cr	No Late Fee	Not applicable
₹2 Cr to ₹5 Cr	₹50 per day	0.04% of turnover in the State/UT
₹5 Cr to ₹20 Cr	₹100 per day	0.04% of turnover in the State/UT
Above ₹20 Cr	₹200 per day	0.5% of turnover in the State/UT

GSTR-9C Late Fees Waiver Notification Applicability 

Scope of the Scheme: The waiver scheme applies to only those taxpayers who have failed to file GSTR-9 earlier. To avail benefits of this scheme, taxpayers have to file the return before March 31, 2025. 

Already Paid Late Fees: No refunds will be issued if the taxpayer has already filed the return with late payment fees. 

Show Cause Notices (SCNs): If any taxpayer has received SCN for not filing of GSTR-9, they can proceed for notice cancellation by filing the return under this scheme before March 31, 2025. 

Already filed GSTR-9: If the GSTR-9 was filed on-time then no additional penalties will be imposed on filing GSTR-9C. 

Paid Penalty for GSTR-9: If the late fees are already paid for filing GSTR-9 then no additional penalties will be imposed on filing GSTR-9C. 

Applicability: This scheme is applicable to the GSTR-9C pending return for FY 2017-18, FY 2018-19, FY 2019-20, FY 2020-21, FY 2021-22, or FY 2022-23.

Also check out the GSTR-9 Filing Process

Over to You

We hope after reading this blog on GSTR-9C late fees waiver you got to know how to wave-off late payments fees on GSTR-9C. We encourage you to make the best use of this scheme and file your pending returns before March 31, 2025 and prevent unnecessary scrutiny from the tax authorities. If you are looking for the best GST return filing software then you should try – Munim Return Filing Software.  

FAQs

1. Is late fee applicable on GSTR 9C?

Yes, late fee is applicable on GSTR-9C but recent notification from CBIC has waived GSTR-9C late fees. 

2. What are GSTR-9 and 9C?​

GSTR-9: It is an annual return filed by the taxpayers revealing details with regards to outward and inward supplies made during the given financial year. 

GSTR-9C: It is a reconciliation statement between GSTR-9 and the audited financial statements. It is filed by the companies whose turnover is Rs. 2 Crores or more. 

3. How do you download an error report in GSTR-9C?

Download the GSTR-9C error report by following the steps explained below: 

Step 1: Log in to the GST portal with your valid credentials 

Step 2: Go to the GSTR-9C tile from the navigation bar 

Step 3: Go to the Upload History table 

Step 4: Click on ‘Generate error report’ link 

Step 5: Click on ‘Download error report’ under the ‘Error Report’ column. 

The error will be downloaded in JSON format. Import this file into your accounting tool to make the required changes. 

4. Who is required to file GSTR-9C​?

GSTR-9C is required to be filed by all the GST-registered taxpayers whose annual turnover is over ₹2 crore. 

5. What is the GSTR-9C reconciliation statement​?

GSTR-9C is a reconciliation statement that compares the values between the annual GSTR-9 and the audited financial statements of the given financial year. 

6. How to file GSTR-9C? 

​Following are the steps to filing GSTR-9C from Munim Return Filing software: 

Step 1: Log in to Munim GST Return Filing Software

Step 2: Now go to the ‘My Company’ tab from the left-hand side of the screen 

Step 3: Import the data either from the system or the GST portal. 

Step 4: Check the imported data and press ‘Save & Next’ to see if the imported data is correct. 

Step 5: Now upload the balance sheet, P&L statement and other required documents (if any). 

Step 6: Now click on ‘Upload Data to GSTN’ 

Step 7: File the return by verifying either with EVC or DSC.