GST Non-Filing Notice: GSTR-3A, Section 46 & Section 62 Assessment Explained

Missing a GST return is not only a late-fee issue. Continued non-filing can move the taxpayer into a statutory notice and best-judgment assessment process. For businesses, finance teams and tax professionals, the critical question is not merely how much late fee is payable, but how quickly the default must be regularised before an estimated tax liability is created by the department.

Direct answer: Section 46 of the Central Goods and Services Tax Act, 2017 provides for a notice to a registered person who fails to furnish a return under sections 39, 44 or 45, requiring the return to be furnished within the prescribed period. If a return under section 39 or section 45 remains unfiled even after the Section 46 notice, Section 62 permits the proper officer to assess the tax liability to the best of judgment. The assessment order under Section 62 is issued in Form GST ASMT-13.

1. What is a GST non-filing notice?

The GST framework distinguishes between a delayed return and persistent non-filing. Section 46 is the statutory notice mechanism for return defaulters. It applies where a registered person fails to furnish a return required under Section 39, the annual return under Section 44, or the final return under Section 45. The notice requires the return to be furnished within fifteen days in the prescribed manner.

Practically, this stage should be treated as an escalation point. The business should immediately identify every pending tax period, reconcile the underlying books and GST data, quantify tax, interest and late fee, and determine whether any separate registration or enforcement issue has also arisen.

2. What happens if the return is still not filed? Section 62 best-judgment assessment

Section 62 applies where a registered person fails to furnish a return under Section 39 or Section 45 even after service of the Section 46 notice. The proper officer may then assess the taxpayer's liability to the best of judgment using relevant material available or gathered by the department.

The procedural rules prescribe Form GST ASMT-13 for the assessment order under Section 62(1). A best-judgment assessment can therefore create a departmental tax demand based on available information rather than the taxpayer's own filed return. That makes passive non-response particularly risky: the estimated liability may not mirror the final liability that would emerge from properly reconciled records.

3. The current 60 + 60 day relief window under Section 62

A particularly important point for current GST compliance is that older references to a 30-day withdrawal window are outdated. Under the current Section 62(2), if the registered person furnishes a valid return within sixty days from service of the best-judgment assessment order, the assessment order is deemed to be withdrawn.

There is also a further sixty-day opportunity. If the taxpayer misses the first sixty days, a valid return may still be furnished within the next sixty days on payment of an additional late fee of ₹100 for each day of delay beyond the first sixty days. If the valid return is furnished within this extended period, the Section 62 assessment order is also deemed to be withdrawn.

This extension was introduced through the Finance Act, 2023 and took effect from 1 October 2023. For advisers reviewing older templates, standard operating procedures or online articles, the distinction matters because a compliance team relying on the previous 30-day position may incorrectly assess the available statutory remedy.

4. What survives even when the ASMT-13 order is withdrawn?

Withdrawal of the best-judgment assessment does not wipe out the financial consequences of late filing. Section 62(2) expressly preserves liability for interest under Section 50(1) and late fee under Section 47. In other words, filing the valid return can remove the estimated Section 62 assessment order, but it does not convert the original filing delay into a compliant filing.

5. A practical example

Assume a registered business has not filed a required return despite the return-defaulter notice and later receives an ASMT-13 order under Section 62. The first priority is to calculate the statutory sixty-day period from the date of service of that assessment order, not from the original return due date. If a valid return is filed within that period, the assessment order is deemed withdrawn, while interest and ordinary late fee continue. If the first window is missed, the business should immediately test the further sixty-day window and quantify the additional ₹100-per-day fee for the delay beyond the first sixty days.

6. How should a business regularise old GST returns after a notice?

A defensible regularisation exercise should ordinarily include the following controls:

• Prepare a period-wise list of every pending return and identify whether the default relates to GSTR-3B, annual/final return obligations or connected statements.

• Reconcile turnover with books, e-invoice/e-way bill data where applicable, GSTR-1, GSTR-2B and tax ledgers before filing. Filing merely to remove the non-filer status without reconciling the tax position can create a second layer of exposure.

• Determine the date of service of the Section 46 notice and, if already issued, the ASMT-13 order. The Section 62 withdrawal window is tied to service of the assessment order.

• Compute tax, Section 50 interest, Section 47 late fee and, where the first sixty-day post-assessment window has expired, the additional ₹100-per-day amount separately. Do not treat these amounts as interchangeable.

• Preserve return acknowledgements, challans, electronic liability/cash/credit ledger extracts and the assessment-order service record in a single compliance file.

• After filing, verify the portal status and confirm whether the Section 62 order has been treated as withdrawn. If the portal or order position does not align with the statutory filing, escalation may be necessary.

7. Section 62 is not the same as a normal GST show-cause dispute

Section 62 is specifically a best-judgment mechanism for specified return non-filers. It should not be confused with a merits-based tax determination proceeding for short payment, wrong input tax credit or other substantive issues. A taxpayer can therefore face more than one compliance track: filing the pending return may address the Section 62 assessment, but a separate discrepancy or tax issue may still need to be answered on its own legal footing.

For a separate guide on responding to substantive GST show-cause notices, see PGT & Associates: https://www.pgtandassociates.com/post/how-to-respond-to-a-gst-show-cause-notice-scn-step-by-step-legal-guide

8. How does this connect with GST late fees?

Late fee is one consequence of delayed filing; GSTR-3A/Section 46 escalation and Section 62 assessment are consequences of continued non-filing. Businesses should therefore not evaluate a backlog only by asking whether the late fee is affordable. The more important question is whether the default has crossed into notice, assessment, registration or recovery risk.

For the separate late-fee mechanics of delayed GSTR-1, GSTR-3B and GSTR-9, see PGT & Associates' GST Late Fee & Penalty guide: https://www.pgtandassociates.com/post/understanding-late-fees-and-penalties-for-delayed-gst-return-filings

9. Frequently asked questions

Does filing the return automatically cancel a Section 62 assessment order?

If a valid return is furnished within the statutory window in Section 62(2), the assessment order is deemed withdrawn. The first window is sixty days from service of the assessment order; an additional sixty-day period is available subject to the prescribed additional late fee.

Does interest disappear when the order is withdrawn?

No. Section 62(2) expressly preserves interest under Section 50(1) and late fee under Section 47 even where the best-judgment order is deemed withdrawn after filing.

What form is used for a Section 62 best-judgment assessment?

The CGST Rules prescribe Form GST ASMT-13 for the assessment order made under Section 62(1).

Can a business ignore a non-filing notice if there was no turnover?

No. A return obligation does not disappear merely because the period had nil or low activity where the registered person is otherwise required to furnish the return. The correct response is to verify the applicable return obligation and regularise it rather than leave the notice unanswered.

10. Practical takeaway for businesses and advisers

The key control is speed with reconciliation. Once non-filing has moved to the Section 46 notice stage, waiting for a demand estimate is usually a poor compliance strategy. Once an ASMT-13 order is served, the sixty-day and extended sixty-day timelines should be docketed immediately, along with the return filing, tax, interest and late-fee workstreams.

If your business has multiple pending GST periods, a return-defaulter notice or an ASMT-13 assessment, PGT & Associates can assist with period-wise reconciliation, return regularisation, interest and late-fee review, and representation on connected GST proceedings.

Primary legal references

Central Goods and Services Tax Act, 2017: Sections 46, 47, 50 and 62. CGST Rules: assessment order under Section 62(1) in Form GST ASMT-13. Current Section 62(2) incorporates the sixty-day withdrawal window and the further sixty-day window with additional late fee.

Disclaimer: This article is for general professional information and does not constitute legal or tax advice. GST consequences depend on the taxpayer's facts, return type, tax period, notices/orders served and subsequent statutory changes. Obtain case-specific advice before acting on a notice or assessment.