Late fee waivers for GSTR-9 and GSTR-10
For a dormant registration with years of unfiled returns, the late fee is usually larger than the tax.
Late fee under Section 47 applies to delayed filing of returns, including the annual return in GSTR-9 and the final return in GSTR-10, subject to the caps and the waivers notified from time to time. Waiver schemes have been notified for specified periods, capping or waiving the late fee where the pending returns are filed within a stated window. Whether a scheme applies to your periods must be verified against the current notifications.
The position
Late fee accrues per day of delay, subject to the statutory and notified caps, which differ by return and by turnover slab.
Waiver and cap schemes have been notified for GSTR-9 and GSTR-10 for specified past periods, requiring filing within a window.
The late fee is not reduced by a successful appeal on the tax; it relates to the filing default.
For a dormant registration with several years pending, the aggregate late fee frequently exceeds any tax, which is why the notification position must be checked before filing.
Practical steps
List every registration and every pending return, with the period and the computed late fee at the current cap.
Check the notification position for each return and period before filing; filing outside a window that is about to open is an avoidable cost.
For registrations no longer required, file GSTR-10 and complete the cancellation rather than leaving the registration dormant, because the exposure grows.
Where a late fee has been paid that a subsequent waiver covered, examine whether a refund is available; generally waivers are prospective in operation and refunds are not granted, so timing matters.
What to do on Monday
List every registration and pending return with the computed late fee before filing anything.
Check the current notification position for each return and period.
Complete cancellation with GSTR-10 for registrations no longer required.
Time the filing to any open window rather than filing immediately.
This page states the general position. A reader with a specific question on their own facts may write to the GST practice at AMLEGALS.
Write to the GST practiceQuestions we are asked on this
Is late fee waived if there was no liability?
Late fee relates to the filing default, not the liability. Nil returns filed late also attract late fee, subject to the lower caps notified.
Does a successful appeal remove the late fee?
No. It is unaffected by the outcome on tax.
Can late fee already paid be refunded under a later waiver?
Generally not; waivers operate prospectively. File at the right time.
Is GSTR-10 mandatory after cancellation?
Yes, within three months of cancellation or of the order, and its non filing carries its own consequences.
How do we find out whether a scheme applies?
Verify against the current notifications for the specific return and period; these have been notified repeatedly with different terms.
In this cluster
- Section 128A: the waiver that is arithmetic, not amnesty
- SPL-01 and SPL-02: filing the Section 128A waiver application correctly
- Withdrawing an appeal to access the waiver: the sequencing risk
- Amnesty for revocation of cancelled registrations
- Should you settle or litigate? A decision framework
- Compounding of offences under Section 138
- Section 128A waiver: the eligibility and savings working sheet
GST Insights is published by AMLEGALS for general information. Law stated as on 3 September 2026. Not advice on any particular set of facts; not an advertisement or a solicitation under Rule 36 of the Bar Council of India Rules. Readers with a question on their own facts may write to the GST practice of their own accord.