Section 47 – Levy of Late Fee

Section 47 of the CGST Act imposes a statutory late fee when a registered person fails to file any GST return within its prescribed due date. The fee arises automatically, applies per day of delay, and continues until the return is furnished. The provision ensures that taxpayers comply with the periodic reporting framework and maintain updated GST records.

How Late Fee is Calculated

The late fee under Section 47 applies on a per-day basis and is levied separately under CGST and SGST. It continues until the pending return is finally furnished.

• Late fee is charged for each day after the due date.
• Payable under both CGST and SGST components.
• Applies to all GST returns (GSTR-1, 3B, 4, 5, 6, 7, 8, 9, etc.).
• Government may issue notifications reducing maximum caps for specific returns or taxpayer classes.
• No exemption merely because tax liability is nil.

Late Fee for Annual Return (GSTR-9)

The late fee for GSTR-9 (Annual Return) is also governed by Section 47. Notifications have rationalised these fees by prescribing turnover-based caps for different classes of taxpayers.

• Where GSTR‑9C is required, the annual return is considered complete only when both GSTR‑9 and GSTR‑9C are filed; late fee runs until that complete filing date.
• The threshold for requiring GSTR‑9C is turnover exceeding ₹5 crore in a financial year, as per official clarification effective 1 Aug 2021.
• Reduced late-fee caps apply as per Government notifications, but the daily late-fee rule still originates from Section 47.

Late Fee When Filing is Delayed Beyond the Due Date

Section 47 continues to operate as long as the return is legally allowed to be filed. The GST portal calculates the total late fee for the delay period, and filing is permitted only after the accumulated amount is paid.

• Late fee is payable up to the last date on which filing is allowed.
• The taxpayer must pay the total late fee accrued before the system accepts the return.
• For annual returns, section 44 provides that filing is not allowed after three years from the due date, unless extended by the Government on Council recommendations.

When the Filing Window is Legally Closed

This is the important extension beyond the core section. Certain GST returns—such as the Annual Return (GSTR-9)—have a legally defined outer time limit (for GSTR-9, it is three years from the original due date). After this final date:

• The return cannot be filed on the portal (unless a special Government order reopens filing).
• Late fee cannot continue beyond this point, because late fee applies only when filing is legally permissible.
• Any late fee accrued up to the last permitted filing date remains payable.

This ensures that late fee under Section 47 applies only within the valid filing window.

Late Fee even after Assessment Proceedings

Your Bare Act clarifies that if the department issues a best-judgment assessment for non-filing and the taxpayer later files the return, the assessment may be withdrawn—but late fee and interest still remain payable. This proves that late fee is independent of assessment proceedings.

Purpose of Section 47

The objective of Section 47 is to promote timely compliance, ensure accurate GST data flow, prevent accumulation of pending returns, and maintain a uniform penalty system. Its application across all types of returns ensures consistency and predictability in the GST compliance environment.

GST Late Fee Table

A. Monthly / Quarterly Returns (GSTR-1, GSTR-3B, GSTR-4, GSTR-5, GSTR-6, GSTR-7, GSTR-8)

B. Annual Return (GSTR-9)

Turnover-based late-fee caps notified by Govt.

Note:

• Daily late fee still arises under Section 47.
• Cap applies only to the maximum payable amount, not the daily rate.

C. Reconciliation Statement

The practical late-fee computation depends on whether GSTR‑9C is required; if required, late fee is tied to the completion of the annual return as clarified officially.

D. NIL Returns

E. Summary Table