GST Amnesty Scheme: Late Fee Waivers and Revocation Rules

Managing tax compliance for a small business is challenging, especially when cash flow constraints force you to delay filing. Under normal GST rules, missing a monthly GSTR-3B deadline triggers a late fee of ₹50 per day (₹20 per day for nil filers), capped at ₹10,000 per return. For annual returns, the late fee is calculated at 0.25% of turnover. These penalties compound quickly, creating insurmountable compliance backlogs for struggling businesses.

To assist such taxpayers and encourage return-filing compliance, the GST Council periodically announces the GST Amnesty Scheme. The scheme provides time-limited windows with reduced or waived late fees, along with special provisions for restoring cancelled registrations.

What is the GST Amnesty Scheme?

The GST Amnesty Scheme is a policy measure notified through CGST Notifications by the Central Board of Indirect Taxes and Customs (CBIC). It provides:

• Capped or waived late fees for overdue return filings for a specified period.
• Extended timelines for filing revocation applications for suo moto cancelled GSTINs.
• Reductions in penalties for specific categories of late filers.

The GST Council has issued multiple amnesty scheme notifications — covering different periods and different return types — since GST's implementation in 2017. Each scheme specifies:

1. The return types covered (e.g., GSTR-1, GSTR-3B, GSTR-4, GSTR-9, GSTR-10).
2. The periods for which the amnesty applies.
3. The dates between which returns must be filed to avail the waiver.
4. The reduced late fee payable (either ₹0, ₹500, or some other capped amount).

Late Fee Waivers by Return Type

The Amnesty Scheme applies specific treatment to different return types:

Interest on Delayed Tax: Is It Waived?

A common misconception is that the GST Amnesty Scheme also waives interest on delayed tax payments. In most amnesty notifications, interest is NOT waived. Under Section 50 of the CGST Act, interest is charged at 18% per annum on the net tax liability not paid by the due date.

The only benefit regarding interest that some amnesty schemes provide is the capping of late fees — not the interest liability itself. Taxpayers wishing to fully clear their compliance backlog must calculate and pay the accrued interest along with their outstanding tax.

Revocation of Suo Moto Cancellations Under Amnesty

If a taxpayer fails to file returns for six consecutive months (or three quarters for composition taxpayers), tax officers can cancel their registration "suo moto." Ordinarily, you must apply for revocation within 30 days of the cancellation order under Rule 23 of the CGST Rules.

The Amnesty Scheme extends this revocation window significantly. Under special amnesty notifications, even taxpayers whose registrations were cancelled years ago can apply for revocation if they:

1. File all pending returns up to the cancellation date using the amnesty reduced late fees.
2. Pay all outstanding tax liabilities and accrued interest.
3. Submit the revocation application (Form GST REG-21) during the active amnesty window.

How to Check If Your GSTIN Is Covered Under Amnesty

To determine if your situation qualifies for an ongoing amnesty benefit:

1. Log in to the GST portal (www.gst.gov.in).
2. Navigate to Services → Returns → View Return Status.
3. Identify all pending return periods.
4. Check the CBIC website or official GST notifications for the currently active amnesty scheme dates and applicable return types.
5. File the overdue returns during the active window; the portal will automatically compute the capped late fee.

Reconstructing Your Books Under Amnesty: The Role of Purchase Automation

Taxpayers seeking to avail of the GST Amnesty Scheme often need to reconstruct months or years of records. This is particularly complex on the purchase side — locating old vendor invoices, entering the right HSN codes, and ensuring the correct GSTIN is on each purchase voucher.

TrulyInvoice dramatically simplifies this process. By reading your vendor invoice PDFs — even old or scanned copies — TrulyInvoice extracts GSTIN, invoice number, date, HSN codes, tax amounts, and item descriptions using OCR. It then pushes formatted F9 purchase vouchers directly into Tally Prime. This allows you to reconstruct missing periods' purchase ledgers rapidly, helping you file all pending GSTR-3B returns accurately before the amnesty window closes. TrulyInvoice is available at a flat plans starting at ₹399/month subscription.