Missed GSTR-9C Filing? CBIC Grants Late Fee Waiver Until March 31, 2025

If you have missed filing your GSTR-9C for the financial years 2017-18 to 2022-23, there is good news for you. The Central Board of Indirect Taxes and Customs (CBIC) has announced a waiver of late fees, provided you file your pending GSTR-9C by March 31, 2025. This initiative offers taxpayers an opportunity to avoid penalties and GST demands that could arise due to non-compliance.

What is GSTR-9C and Its Importance

GSTR-9C is an important annual GST reconciliation statement that every taxpayer with an aggregate turnover exceeding Rs.5 crore must file. It serves as a reconciliation between the details provided in GSTR-9 (the annual return) and the audited financial statements of the taxpayer. The purpose of this reconciliation is to ensure the accuracy of the GST filings and verify that the declared figures match with the audited accounts.

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

Generally, the deadline for filing GSTR-9C coincides with the GSTR-9 submission date, which is December 31 of the following financial year. For instance, the due date for FY 2023-24 will be December 31, 2024. However, for the financial years 2017-18 to 2022-23, the CBIC has provided relief by waiving the late fees if taxpayers submit their GSTR-9C by March 31, 2025.

CBIC's Notification on GSTR-9C Late Fee Waiver

On January 23, 2025, CBIC issued Notification No. 8/2025, which provides a waiver of late fees for taxpayers who have not filed their GSTR-9C along with their GSTR-9 for the financial years 2017-18 to 2022-23. This waiver allows taxpayers to submit their pending filings without incurring penalties, ensuring compliance without unnecessary financial burden. However, taxpayers must note that any late fees already paid will not be refunded.

Key Conditions for Late Fee Waiver

To qualify for this late fee waiver, the following conditions must be met:

• Timely GSTR-9 Filing: If the taxpayer has filed their GSTR-9 before the deadline, they will not be liable for late fees related to GSTR-9C for the mentioned financial years.

• Late GSTR-9 Filing with Fees Paid: If a taxpayer filed GSTR-9 late and paid the applicable fees, no additional late fees will be imposed for GSTR-9C.

• Handling of Show Cause Notices (SCNs): The GST department had previously issued Show Cause Notices (SCNs) for delayed GSTR-9C filings. Taxpayers can now request the GST proper officer to cancel such notices upon submission of their pending returns before March 31, 2025.

Consequences of Failing to File GSTR-9C Before March 31, 2025

If a taxpayer fails to file GSTR-9C by the extended deadline, they may face serious consequences, including:

• Issuance of Show Cause Notices (SCNs): The GST department may issue SCNs under:

• Section 73 for non-fraudulent discrepancies

• Section 74 for fraudulent activities

• Monetary Penalties:

• General penalty of up to Rs.25,000 under Section 125 of the CGST Act

• Additional penalties under State GST laws, effectively doubling the financial impact

• Late fees accumulating with further delay

• GST Audits and Assessments: Authorities may initiate audits, inspections, or searches, leading to additional scrutiny of business transactions, potential tax demands, or legal actions.

• Reputational and Business Risks: Continued non-compliance may negatively impact a taxpayer's business reputation, potentially leading to GST registration suspension or cancellation.

How to File GSTR-9C: Step-by-Step Guide

To ensure compliance, taxpayers must follow these steps to file GSTR-9C correctly:

Step 1: Pre-requisites for GSTR-9C Filing

Before filing, ensure the following requirements are met:

• Valid GST Registration (GSTIN)

• Active Login Credentials for the GST portal

• Prior submission of GSTR-9 for the financial year in question

• Aggregate turnover exceeding Rs.5 crore in the relevant financial year

Step 2: Prepare GSTR-9C Using Offline Utility

1. Download the Required Forms:

• Log in to the GST Portal

• Download GSTR-9C Tables derived from GSTR-9

2. Download the GSTR-9C Offline Tool:

• Navigate to the Downloads section

• Select GSTR-9C Offline Tool

3. Prepare GSTR-9C Statement:

• Enter relevant data in the offline tool

• Generate a preview PDF to review before submission

• Create a JSON file for upload

Step 3: Upload the GSTR-9C JSON File to the GST Portal

1. Login and Navigate to Returns:

• Log in to the GST portal

• Select Annual Return for the relevant financial year

2. Upload the JSON File:

• Click Prepare Offline

• Upload the generated JSON file

• If errors are detected, download the Error Report, correct them, and re-upload

Step 4: File GSTR-9C on the GST Portal

1. Upload Financial Statements:

• Balance Sheet & Profit & Loss Statement (PDF, max 5MB per file)

2. Proceed to File:

• Click PROCEED TO FILE

• Review draft submission using PREVIEW DRAFT GSTR-9C

• Click FILE GSTR-9C to complete the process

3. Track Submission Status:

• Navigate to Services > Returns > View Filed Returns to check the status

What Should Taxpayers Do Now?

1. File GSTR-9C Before March 31, 2025: Ensure that all pending GSTR-9C filings from 2017-18 to 2022-23 are submitted to avail the late fee waiver.

2. Handle Show Cause Notices (SCNs): If you have received an SCN, submit GSTR-9C and request the GST officer to cancel the notice.

3. Upgrade GST Compliance Systems: Consider using automated tools for GST reconciliation and compliance management to avoid delays in the future.

Get Compliance Calendar Assistance for Filing GSTR-9C

Filing GSTR-9C can be a complex process requiring accuracy and reconciliation with audited financial statements. To ensure a hassle-free experience and avoid penalties, it is advisable to seek expert guidance. Professional services can help with timely filing, error rectification, and compliance adherence, allowing you to focus on business growth without regulatory stress.

For assistance, contact Compliance Calendar GST experts today and ensure your GSTR-9C filings are completed on time!

FAQs

Q1. What is GSTR-9C, and who needs to file it?

Ans. GSTR-9C is an annual GST reconciliation statement required to be filed by taxpayers whose aggregate turnover exceeds Rs.5 Crore in a financial year. It acts as a comparison between the figures reported in GSTR-9 (Annual Return) and the taxpayer’s audited financial statements to ensure accuracy in GST declarations.

Q2. What is the latest CBIC notification on the waiver of late fees for GSTR-9C filing?

Ans. On January 23, 2025, the Central Board of Indirect Taxes and Customs (CBIC) issued Notification No. 8/2025, announcing a waiver of late fees for missed GSTR-9C filings for FY 2017-18 to 2022-23. Taxpayers can avail of this waiver if they submit their pending GSTR-9C by March 31, 2025. However, late fees already paid will not be refunded.

Q3. What happens if I do not file GSTR-9C before March 31, 2025?

Ans. If you fail to file GSTR-9C by March 31, 2025, the following consequences may arise:\n

• Late fees and penalties under Section 125 of the CGST Act (up to Rs.25,000) and equivalent State GST penalties.

• GST audits, inspections, and assessments by the tax department.

• Issuance of Show Cause Notices (SCNs) under Section 73 (non-fraudulent cases) or Section 74 (fraudulent cases).

• Additional compliance burdens and scrutiny of your business transactions.

To avoid these consequences, it is recommended to file GSTR-9C before the March 31, 2025 deadline.

Q4. If I have already paid a late fee for GSTR-9C, will I get a refund?

Ans. No, the waiver does not apply retroactively. If you have already paid a late fee for delayed GSTR-9C filings in the past, CBIC has clarified that no refunds will be provided. However, you can still avoid additional late fees by ensuring that any remaining pending GSTR-9C filings for FY 2017-18 to 2022-23 are submitted before March 31, 2025.

Q5. How can I file my pending GSTR-9C to avail of the late fee waiver?

Ans. To file GSTR-9C, follow these steps:

1. Log in to the GST Portal using your GSTIN and credentials.

2. Download the GSTR-9C Offline Tool from the GST portal.

3. Fill in the required data in the offline tool and generate a JSON file.

4. Upload the JSON file to the GST portal under “Annual Returns.”

5. Attach financial statements (Balance Sheet, Profit & Loss Statement in PDF format).

6. Preview the GSTR-9C form and click “Proceed to File.”

7. Submit the form using DSC or EVC to complete the filing process.

Q6. Can I request the cancellation of a Show Cause Notice (SCN) related to late GSTR-9C filing?

Ans. Yes. If you have received a Show Cause Notice (SCN) for non-filing or late filing of GSTR-9C, you can now request the GST officer to cancel the notice after submitting the pending GSTR-9C by March 31, 2025. This waiver helps taxpayers avoid unnecessary tax demands and penalties.

Q7. What documents are required to file GSTR-9C?

Ans. To successfully file GSTR-9C, you must have the following documents ready:

• Audited financial statements for the relevant financial year.

• Annual GST Return (GSTR-9) already filed for the respective year.

• A JSON file generated using the GSTR-9C Offline Tool.

• Balance Sheet and Profit & Loss Statement (PDF format, max 5MB per file).

• GST Portal login credentials to access the return filing section.