CBIC Waives GSTR-9C Late Fees – File by March 31, 2025!

Introduction

If you haven’t filed your GSTR-9C for any financial year from 2017-18 to 2022-23, there’s good news — the CBIC has announced a late fee waiver for these pending filings. To benefit from this relief, you must complete the filing by March 31, 2025.

Once filed, you can request the GST proper officer to withdraw any issued Show Cause Notices (SCNs) and halt further GST proceedings

File Your Pending GSTR-9C by March 31, 2025, to Avoid Late Fees

On January 23, 2025, the CBIC issued Notification No. 8/2025, offering relief for taxpayers who missed filing GSTR-9C along with GSTR-9 for FY 2017-18 to 2022-23.

If GSTR-9C is submitted by March 31, 2025, the late fee will only be calculated up to the actual filing date. However, late fees already paid will not be refunded

What is GSTR-9?

GSTR-9 is the annual return that most registered taxpayers must file under the GST regime. It includes a consolidated summary of monthly/quarterly GST returns filed during the year.

Who Must File?
All registered persons, except Input Service Distributors (ISDs), TDS/TCS deductors, casual taxable persons, and non-residents.
Threshold:
Applicable for those with an aggregate turnover exceeding ₹2 crore in a financial year.
Due Date:
By December 31 following the end of the financial year

What is GSTR-9C?

GSTR-9C is an annual GST reconciliation statement that must be filed by eligible taxpayers. It provides a detailed comparison between the data reported in the annual return (Form GSTR-9) and the figures in the taxpayer’s audited financial statements, ensuring accuracy and compliance in GST reporting.

Who is Required to File GSTR-9C?

All registered taxpayers with an annual aggregate turnover exceeding ₹5 Crore in a financial year are mandated to file GSTR-9C. Along with the reconciliation statement, they must also submit their audited annual financial statements to validate the accuracy and integrity of the GST data reported

Why GSTR-9C Matters

GSTR-9C plays a critical role in ensuring GST compliance by serving as an annual reconciliation statement. It highlights and explains any mismatches between the figures reported in the GST returns—such as sales, taxes, and input tax credits—and those recorded in the audited financial statements. By providing a clear justification for these discrepancies, GSTR-9C helps the GST authorities verify the accuracy of the returns and supports transparent, self-certified compliance by the taxpayer

Purpose of Filing GSTR-9C

GSTR-9C is a mandatory reconciliation statement required under Section 44(2) of the CGST Act, 2017 for taxpayers with an annual aggregate turnover exceeding ₹5 Crore. Filed alongside the GSTR-9 annual return, GSTR-9C compares the data reported in the GST returns with the figures in the taxpayer’s audited financial statements. Its primary purpose is to identify any inconsistencies and validate the accuracy of GST declarations, thereby ensuring transparency and compliance with GST regulations

What is the Due Date for Filing GSTR-9C?

The due date for filing GSTR-9C aligns with the deadline for submitting the annual return in GSTR-9. Taxpayers must file GSTR-9C on or before December 31 of the year following the financial year under audit.

For example, for the financial year 2023-24, the GSTR-9C must be filed by December 31, 2024. Timely filing is crucial to remain compliant with GST laws and to avoid penalties for late submission.

Additionally, the CBIC has announced a waiver of late fees for GSTR-9C filings for the financial years 2017-18 to 2022-23. To benefit from this waiver and avoid GST notices, taxpayers must file their pending GSTR-9C forms by March 31, 2025

Conditions for Waiver of Late Fees for GSTR-9C Filing

The recent notification provides a waiver of late fees for filing GSTR-9C for the financial years 2017-18 to 2022-23, subject to the following conditions:

On-Time GSTR-9 Filing: If a taxpayer has submitted their GSTR-9 by the due date, no late fees will be charged for the corresponding GSTR-9C filings for these financial years.
Late GSTR-9 Filing with Fees Paid: If GSTR-9 was filed after the deadline but the taxpayer has already paid the applicable late fees, no additional late fees will be levied for GSTR-9C separately.
Handling Show Cause Notices (SCNs): Previously, GST authorities issued Show Cause Notices for non-payment of late fees on delayed GSTR-9C filings. Under this new notification, taxpayers can now request the GST proper officer to cancel such SCNs, effectively stopping any GST demands related to late filing

Consequences of Not Filing GSTR-9C by March 31, 2025

If a GST-registered taxpayer fails to file the GSTR-9C return by the final deadline of March 31, 2025—even after filing GSTR-1 and GSTR-3B with proper reconciliation against GSTR-2A and GSTR-2B—the GST authorities may take strict action. During audits, inspections, or return scrutiny, the department could initiate proceedings if discrepancies are found in outward supplies, tax liabilities, or Input Tax Credit (ITC) claims, especially under the Reverse Charge Mechanism (RCM).

Issuance of Notices
The GST department will typically issue a Show Cause Notice (SCN) demanding the filing of GSTR-9C within a given timeframe. This SCN may be issued under:

Section 73 for non-fraudulent discrepancies, or
Section 74 for cases involving fraud.

Penalties

Monetary Penalties: Failure to file GSTR-9C can result in penalties up to ₹25,000 under Section 125 of the CGST Act.
State GST Penalties: Additional penalties may be imposed under respective State GST laws, potentially increasing the overall financial burden.
Late Fees: Delayed filing attracts late fees, adding to the taxpayer’s liabilities.

Further Actions by GST Authorities

The department may initiate audits or assessments to closely examine the taxpayer’s filings for inconsistencies or non-compliance.
Continued non-filing can lead to increased scrutiny, possibly resulting in allegations of fraud or tax evasion, escalating the legal and financial risks for the taxpayer

GSTR-9C Submission Process

GSTR-9C must be filed online through the GST portal or at a facilitation centre, along with:

A copy of the audited financial statements
The Annual Return filed in Form GSTR-9

Pre-requisites to Prepare and File GSTR-9C

To file GSTR-9C successfully, ensure the following prerequisites are met:

Valid GST Registration: You must have a valid GSTIN and be registered under GST.
Active Login Credentials: Your GST portal username and password should be current and functional.
Filing of GSTR-9: The Annual Return (Form GSTR-9) for the relevant financial year must be filed.
Aggregate Turnover: Your business turnover should exceed ₹5 Crore during the financial year

Procedure to File GSTR-9C

Filing GSTR-9C is a key compliance step for eligible taxpayers. Follow these steps for a smooth filing process:

How to Generate and Upload GSTR-9C JSON File Using the Offline Utility

Download Necessary Forms and Tables:
Log in to the GST portal with your GSTIN and credentials. Download Form GSTR-9 and the GSTR-9C tables for the relevant financial year.
Download the GSTR-9C Offline Tool:
Navigate to the “Downloads” tab on the GST portal, select “Offline Tools,” and download the “GSTR-9C Offline Tool.”
Prepare the GSTR-9C Statement:
Open the offline utility worksheet, enter the required data into the tables, and generate a PDF preview to review the draft. Once finalized, create the JSON file.

Steps to Upload the GSTR-9C JSON File on the GST Portal

Login and Navigate to Returns:
Log in to the GST portal. Under the “Returns” tab, select “Annual Return,” choose the financial year, and click “Search.”
Prepare for Upload:
Click on “Prepare Offline,” then select “Upload” to begin uploading the JSON file.
Upload and Edit (if necessary):
Upload your JSON file. If there are any errors or required changes, make edits in the offline tool, regenerate the JSON file, and re-upload.
Error Handling:
If errors appear during upload, download the Error Report, fix the issues, and upload the corrected JSON file again.

Steps to Complete Filing GSTR-9C on the GST Portal

Upload Financial Statements:
Upload relevant financial documents such as the Balance Sheet and Profit & Loss Statement in PDF format. Each file should be under 5 MB, with a maximum of two files per section.
Save Each Document:
After uploading, click “SAVE” for each document to confirm. The status should change to “Processed.” Failure to save will cause errors when filing.
Proceed to File:
Once all documents are uploaded and saved, the “PROCEED TO FILE” button activates. Preview the draft by clicking “PREVIEW DRAFT GSTR-9C.”
File the Return:
After verification, click “PROCEED TO FILE,” confirm your details, and select “FILE GSTR-9C” to submit.

Track Filed Returns

After filing, track your submission status by going to the “Services” tab, selecting “Returns,” and then “View Filed Returns.”

Troubleshooting Tips

Error Handling: If you encounter errors in your JSON file upload, download the Error Report, correct the issues, and re-upload the file to ensure successful submission

Practical Steps for Taxpayers:

File GSTR-9C Without Delay: Make sure to submit any outstanding GSTR-9C returns for the financial years 2017-18 to 2022-23 by March 31, 2025, to take advantage of the late fee waiver.
Respond to Show Cause Notices (SCNs): If you have received an SCN for delayed GSTR-9C filing, use this opportunity to request its cancellation by contacting the GST proper officer.
Enhance Compliance Systems: Consider adopting automated solutions like IndiaFilings’s Ledgers to simplify your GST compliance, ensure timely submissions, and minimize the risk of penalties.

By following these steps, taxpayers can efficiently manage their GST responsibilities, avoid unnecessary fines, and ensure smooth business operations

Get Professional Assistance for Filing Your GSTR-9C!

Filing GSTR-9C can be complicated and time-consuming, but you don’t have to handle it on your own. Rely on expert support to ensure your reconciliation statements are accurate and submitted punctually, reducing the risk of errors and penalties. Let our specialists take care of your GSTR-9C filings efficiently, so you can concentrate on growing your business with confidence

About the Author

Rohan

Rohan is a skilled writer who excels at simplifying complex legal concepts into clear, practical guidance. Her articles equip entrepreneurs with the essential knowledge to confidently navigate business laws, helping them successfully start and manage their ventures

June 26, 2025