Section 47 CGST Act — GST Late Fee, GSTR-3B, GSTR-1 & GSTR-9 Late Filing

1. Why Section 47 matters

Searches such as “Section 47 CGST Act”, “GST late fee”, “GSTR-3B late fee”, “GSTR-1 late fee”, “GSTR-9 late fee”, “GSTR-10 late fee”, “GSTR-9C late fee” and “GST late filing penalty” all concern one core question: what monetary consequence arises when a GST return or statement is filed after its due date?

Section 47 is the CGST Act's principal late-fee provision. But a correct answer requires more than quoting the ₹100-per-day statutory language. The Government has repeatedly used its notification powers to waive or rationalise late fees for particular returns, taxpayers, financial years and periods.

2. What Section 47 means

Section 47 imposes late fee where specified GST details, statements or returns are not furnished by the prescribed due date.

The original statutory framework contains two principal parts:

India Code's text records the statutory ₹100-per-day framework and the respective maximums, while actual late-fee relief/rationalisation can be prescribed separately by notification. citeturn0search3

3. Statutory structure

The key distinction is between periodic/statutory returns and statements covered by Section 47(1) and the annual return covered by Section 47(2).

4. Section 47(1): outward/inward details and returns

Section 47(1) covers failure to furnish the details required under Sections 37 or 38 and specified returns under Sections 39 or 45 by the due date.

The statutory text provides a late fee of ₹100 for every day during which the failure continues, subject to a maximum of ₹5,000. citeturn0search3

However, this statutory figure should not automatically be used as the amount appearing on the GST Portal for every return. Government notifications have repeatedly reduced or waived late fees for particular forms and periods.

5. Section 47(2): annual return

Section 47(2) separately covers failure to furnish the annual return under Section 44. The statutory provision states ₹100 per day, subject to a maximum calculated at 0.25% of turnover in the State or Union territory. citeturn0search3

For current practical filing, however, the taxpayer must also consider the notified rationalisation of late fee for GSTR-9 and any special waiver applicable to the relevant financial year.

6. Statutory rate vs actual payable late fee

This is one of the most important points in Section 47 research.

7. GSTR-1 late fee

GSTR-1 is the outward-supply statement under Section 37 and the Rules. Its delayed filing falls within the Section 47 framework, subject to the applicable notified late-fee treatment.

For a late GSTR-1 working, capture:

• original due date;
• actual filing date;
• number of delayed days;
• taxpayer's filing frequency;
• nil/normal return status where relevant; and
• any waiver or rationalisation notification applicable to the period.

8. GSTR-3B late fee

GSTR-3B is the regular taxpayer's periodic return framework under Section 39. Delayed filing can attract late fee under Section 47, in addition to interest where tax is paid late.

Late fee and interest are different:

9. GSTR-9 late fee

GSTR-9 is the annual return under Section 44. Its late fee is governed by Section 47(2), subject to the notified rationalisation for applicable financial years.

Notification No. 07/2023-Central Tax dated 31 March 2023 rationalised the late fee for GSTR-9 from FY 2022-23 onwards. For aggregate turnover up to ₹5 crore, the notified amount was ₹25 per day subject to a maximum of 0.02% of turnover in the State/UT; for turnover above ₹5 crore and up to ₹20 crore, ₹50 per day subject to the same 0.02% ceiling; and for turnover above ₹20 crore, ₹100 per day subject to a 0.25% ceiling. citeturn2search21turn2search6

These are notification-based amounts, not a rewriting of the basic Section 47(2) statutory text.

10. GSTR-9C late fee

GSTR-9C requires special attention. There is no separate standalone late-fee subsection titled “GSTR-9C late fee” in Section 47. The issue is whether the annual return under Section 44 is complete when GSTR-9C is required.

CBIC Circular No. 246/03/2025-GST clarified that where GSTR-9C is required, the complete annual return consists of GSTR-9 and GSTR-9C. Section 47(2) late fee applies from the annual-return due date until the complete annual return is furnished. citeturn1search25turn1search24

11. GSTR-10 late fee

GSTR-10 is the final return under Section 45. Delayed filing falls within Section 47(1).

The statutory framework provides ₹100 per day subject to the statutory maximum, but specific notifications can waive/reduce late fee for identified periods. For example, Notification No. 08/2023-Central Tax provided a specific historical relief for delayed GSTR-10 filings made during the notified amnesty period.

Therefore, current GSTR-10 late fee should be calculated using the applicable law and notification for the cancellation/final-return period.

12. Other returns/statements

13. Nil-return situations

Nil activity does not automatically mean that late fee is irrelevant. Where a return is required to be filed, failure to file it by the due date can attract the applicable late fee, subject to the specific waiver/rationalisation applicable to that form and period.

Government notifications have historically provided different late-fee treatment for nil returns in certain circumstances. Always check the notification rather than assuming the standard amount.

14. Turnover-based caps

Turnover can be relevant to the maximum late fee for annual returns because Section 47(2) itself expresses the statutory maximum as a percentage of turnover in the State/UT. Notification 07/2023 further rationalised the payable amount for GSTR-9 using turnover slabs for FY 2022-23 onwards. citeturn2search21

Do not confuse:

• aggregate turnover used to classify the taxpayer under a notification; and
• turnover in the State or Union territory used in the statutory percentage cap.

15. Late-fee notifications and waivers

Section 47 should always be researched together with notifications issued under the Government's power to waive late fee.

16. Notification 07/2023-Central Tax

Notification 07/2023-Central Tax dated 31 March 2023 is a major reference for current GSTR-9 late-fee research.

The notification also provided a historical amnesty for specified GSTR-9 non-filers for FY 2017-18 through FY 2021-22, subject to its conditions and filing window. citeturn2search21turn2search2

17. GSTR-9C clarification 2025

Circular No. 246/03/2025-GST dated 30 January 2025 is particularly important when preparing Section 47 content today.

It clarifies that when GSTR-9C is required, the annual return is not complete until both GSTR-9 and GSTR-9C are furnished. Consequently, Section 47(2) late fee runs from the annual-return due date to the date on which the complete annual return is furnished. citeturn1search25

Notification No. 08/2025-Central Tax provided a specific waiver of excess late fee for certain delayed GSTR-9C filings relating to financial years up to FY 2022-23 where the prescribed conditions were satisfied by 31 March 2025. This was a historical concession and should not be presented as a current blanket waiver. citeturn1search9

18. Historical amnesties

GST has used Section 128 and related notification powers to waive or reduce late fee for specific periods. Examples include COVID-period relief, annual-return amnesties and GSTR-10 relief.

These measures illustrate an important legal distinction:

Section 47 creates the late-fee liability → Section 128/notification can waive or reduce it for a specified class and period.

Therefore, an old amnesty should never be described as a permanent exemption from Section 47.

19. Late fee vs interest

A taxpayer can therefore face both late fee and interest on a delayed GSTR-3B where tax was also paid late.

20. Late fee vs penalty

Late fee is not synonymous with penalty.

Late fee generally arises automatically from delayed filing under Section 47, subject to statutory and notified limits. Penalty generally arises under a separate provision and requires the legal conditions of that provision to be satisfied.

For example, a late GSTR-3B may generate late fee and interest without every delayed return automatically resulting in a separate penalty proceeding.

21. Section 46 notice

Section 46 provides a notice to a registered person who fails to furnish a return under Sections 39, 44 or 45. Rule 68 prescribes FORM GSTR-3A and gives the defaulting taxpayer 15 days to furnish the return.

Thus:

Due date missed → Section 47 late fee exposure + possible Section 46 notice → continued non-filing → possible Section 62 assessment.

22. Section 62 assessment

For specified non-filers who continue to default after the Section 46 notice, Section 62 permits best-judgment assessment.

Current Section 62 also provides a mechanism by which a valid return furnished within the statutory period after the assessment order can cause the assessment order to be deemed withdrawn, while interest and late-fee liabilities continue. The period was extended from 30 days to 60 days from 1 October 2023, with a further 60-day opportunity subject to additional late fee under the amended provision. citeturn0search4

23. Accounting for late fee

For internal accounting, late fee is generally treated separately from GST tax liability and interest. The finance team should reconcile the amount paid through the electronic cash ledger and retain the portal challan/return evidence.

For management reporting, track late fee by GSTIN, return, period, cause and responsible process owner so recurring defaults can be eliminated.

24. Multiple GSTINs

Late fee is return-specific and registration-specific. A company with multiple GST registrations should maintain a GSTIN-wise late-fee tracker.

25. Construction and infrastructure examples

For construction, mining, roads, irrigation and infrastructure businesses, late-filing exposure can arise when site data, RA bills, subcontractor invoices or RCM workings are received late.

26. Detailed practical examples

Example 1 — GSTR-3B filed 10 days late

Calculate the applicable late fee using the statutory framework and any notification applicable to the return period. Separately calculate interest if tax was paid late.

Example 2 — nil GSTR-3B

A taxpayer with no outward tax and no ITC still fails to file. Check the nil-return late-fee treatment applicable to that period rather than assuming zero late fee.

Example 3 — GSTR-1 delayed

The sales team closes invoices late and GSTR-1 is filed after the due date. Record the delay and applicable late fee separately from any GSTR-3B interest.

Example 4 — GSTR-9 delayed

For FY 2024-25, the taxpayer files GSTR-9 late. Determine the applicable annual-return late fee under Section 47(2) and the operative notification framework.

Example 5 — GSTR-9C filed after GSTR-9

Where GSTR-9C is required, the complete annual return is not complete until GSTR-9C is filed. Apply the Circular 246/03/2025-GST methodology.

Example 6 — GSTR-10 delayed

A cancelled GSTIN files GSTR-10 after the three-month deadline. Check Section 47(1) and any applicable notification before determining the amount.

Example 7 — historical amnesty

A taxpayer researching a 2021-22 GSTR-9 default should check whether the 2023 amnesty conditions were satisfied; an old waiver cannot be applied to a new default automatically.

Example 8 — interest without late fee

A return is filed on time but tax is paid later. Interest may apply even though there is no late-filing fee because the return itself was timely.

Example 9 — late return plus Section 46

A taxpayer ignores the return until a GSTR-3A notice arrives. Late fee continues as applicable, and the taxpayer also faces escalation risk under the return-default provisions.

Example 10 — infrastructure company

A large contractor has delayed site data across multiple GSTINs. The central tax team uses a return dashboard to identify filing risk, calculate late fee and prevent repeat defaults.

27. Legislative timeline

28. Legal authorities to check

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29. Professional workflow

30. Internal controls

31. Common mistakes

• Quoting ₹100 per day as the universal current GST late fee.
• Ignoring notifications issued under the Government's waiver powers.
• Confusing late fee with interest.
• Confusing late fee with penalty.
• Applying GSTR-9 late-fee slabs to GSTR-3B.
• Applying an old amnesty to a current default.
• Ignoring GSTR-9C when it is required.
• Calculating annual-return late fee without considering the complete GSTR-9/GSTR-9C filing position.
• Not maintaining GSTIN-wise late-fee records.
• Failing to preserve the notification relied upon for a waiver or reduction.

32. Section 47 GST FAQs

What is Section 47 of the CGST Act?

Section 47 is the principal CGST Act provision imposing late fee for specified GST details, statements and returns furnished after the prescribed due date.

What is the late fee under Section 47?

The statutory text provides ₹100 per day for specified Section 47(1) defaults, subject to a maximum of ₹5,000, and ₹100 per day for the annual return under Section 47(2), subject to the statutory turnover-based maximum. Government notifications can waive or rationalise these amounts for specified periods/forms.

What is the GSTR-3B late fee?

GSTR-3B late fee falls within the Section 47 framework applicable to the Section 39 return, but the actual amount should be checked against the notifications applicable to the relevant return period.

What is the GSTR-1 late fee?

GSTR-1 is the Section 37 outward-supply statement and delayed filing can attract Section 47 late fee, subject to applicable notifications.

What is the GSTR-9 late fee?

GSTR-9 is covered by Section 47(2). Notification 07/2023-Central Tax rationalised the late fee for FY 2022-23 onwards using turnover slabs.

Does GSTR-9C have a separate late fee?

Section 47 does not contain a separate standalone GSTR-9C late-fee subsection. Circular 246/03/2025-GST clarifies that where GSTR-9C is required, the complete annual return includes GSTR-9 and GSTR-9C, and Section 47(2) late fee applies until the complete annual return is furnished.

What is the GSTR-10 late fee?

GSTR-10 is the final return under Section 45 and its delayed filing falls within Section 47(1), subject to the statutory maximum and any applicable notification.

Is late fee the same as interest?

No. Late fee is principally linked to delayed filing; interest under Section 50 is linked to delayed payment of tax, subject to the applicable provisions.

Is late fee the same as penalty?

No. Penalty is imposed under separate statutory provisions when their conditions are satisfied.

Can late fee be waived?

Yes, the Government can issue notifications under the relevant statutory power granting specified waivers or reductions. Such relief is normally limited by return type, taxpayer class, financial year and filing window.

Can the GST Portal calculate late fee automatically?

The portal can compute/display applicable late-fee amounts, but a professional working should still understand the statutory provision and notification basis, especially where historical periods or special waivers are involved.

Does a nil return attract late fee?

A required return can attract late fee even when there is no tax liability, subject to the specific notified treatment for the form and period.

What happens if I ignore the late fee?

The late fee remains part of the return liability and continued non-filing can lead to Section 46 notice and, in applicable cases, Section 62 assessment.

33. Related provisions