Section 47 of the Central Goods and Services Tax Act, 2017 deals with the levy of late fee for delayed furnishing of specified GST returns, statements and details. The provision is intended to encourage timely compliance by making a registered person liable to pay a prescribed late fee when the relevant filing is not completed by its due date.
Late fee is different from interest and penalty. Late fee is generally linked to the delay in furnishing a specified return, statement or details, while interest is connected with delayed payment of tax and penalties arise from specified contraventions under the GST law.
The statutory rate in Section 47 provides the basic framework, but the actual amount payable for particular GST returns can be modified or waived through notifications issued under the powers provided by the CGST Act. For this reason, taxpayers should distinguish between the statutory provision in Section 47 and the effective late-fee amounts applicable to a particular return and period. The Government has issued several notifications rationalising or waiving late fees for specific returns, taxpayer classes and periods.
Section 47 is therefore an important provision for understanding the financial consequences of delayed GST compliance.
What Is Section 47 of the CGST Act?
Section 47 is titled:
“Levy of late fee.”
The provision creates a liability for late fee when specified GST filing requirements are not completed by the prescribed due date.
The section contains two principal provisions:
- Section 47(1) deals with specified details and returns other than the annual return covered by Section 44.
- Section 47(2) deals specifically with the return required under Section 44, which is the annual return.
The original statutory wording of Section 47(1) provides a late fee of ₹100 per day for each day during which the specified failure continues, subject to a maximum of ₹5,000. Section 47(2) provides ₹100 per day for delayed furnishing of the annual return, subject to a maximum based on 0.25% of turnover in the State or Union territory.
However, these statutory amounts should not automatically be treated as the amount payable for every GST return today. The Government has used Section 128 and other relevant powers to rationalise or waive late fees for particular forms and circumstances.
Why Is Late Fee Charged Under GST?
GST operates through a return-based compliance system. Taxpayers are required to furnish various returns, statements and details within prescribed time limits.
Timely filing is important because GST compliance involves:
- reporting outward supplies;
- reporting relevant inward-supply information;
- declaring tax liability;
- claiming input tax credit where eligible;
- paying tax;
- reporting annual information; and
- maintaining a continuous electronic compliance record.
If taxpayers could routinely delay these filings without any financial consequence, the effectiveness of the return system could be reduced.
Section 47 therefore provides a statutory mechanism for charging late fee when specified filing requirements are not met on time.
Section 47(1) – Late Fee for Specified Returns and Details
Section 47(1) covers failure to furnish specified details or returns by the due date.
The statutory provision refers to:
- details of outward supplies required under Section 37;
- details of inward supplies required under Section 38;
- returns required under Section 39; and
- returns required under Section 45.
The statutory text provides a late fee of ₹100 for every day during which the failure continues, subject to a maximum of ₹5,000.
The important point is that Section 47(1) provides the statutory framework, while notifications can reduce or waive the amount applicable to particular forms or periods.
Section 47(2) – Late Fee for Annual Return
Section 47(2) specifically deals with delay in furnishing the return required under Section 44.
Section 44 deals with the GST annual return.
Under the statutory wording of Section 47(2), a registered person who fails to furnish the annual return by the due date is liable to a late fee of ₹100 for every day during which the failure continues, subject to a maximum amount calculated at 0.25% of turnover in the relevant State or Union territory.
The effective late fee for annual returns has subsequently been rationalised through notifications for specified classes of taxpayers and financial years.
Therefore, the statutory wording should be read together with the relevant notifications applicable to the financial year and taxpayer category.
Section 47 and GSTR-1
GSTR-1 is the statement used by applicable taxpayers to furnish details of outward supplies.
Historically, delayed filing of GSTR-1 attracted late fee under Section 47.
The Government subsequently rationalised the late fee for delayed GSTR-1 filing through notifications.
For example, Notification No. 20/2021-Central Tax reduced the effective late-fee burden for specified classes of taxpayers filing GSTR-1 from the tax periods beginning June 2021 or the relevant quarter. The notification provided different caps depending on whether the taxpayer had nil outward supplies and depending on turnover categories.
This demonstrates an important principle:
The amount mentioned in Section 47 is the statutory starting point, but the amount actually payable can be affected by subsequent notifications.
Section 47 and GSTR-3B
GSTR-3B is a return filed by applicable taxpayers for reporting GST liability and other relevant information.
Delayed filing of GSTR-3B can attract late fee under Section 47.
The GST Council has noted that the late fee for delayed GSTR-3B filing is system-computed based on the number of days of delay and is reflected in the GST return process.
The Government has also issued notifications rationalising the late fee for GSTR-3B for specified taxpayers and periods.
Therefore, while Section 47 establishes the liability, taxpayers should check the applicable notification-based relief or cap rather than assuming that the maximum statutory amount automatically applies.
Section 47 and GSTR-4
GSTR-4 relates to taxpayers under the composition scheme as prescribed under the GST framework.
Late filing of GSTR-4 can also attract late fee under Section 47, subject to the applicable statutory provisions and notifications.
Notification No. 21/2021-Central Tax provided a rationalised late-fee cap for delayed filing of GSTR-4 from financial year 2021-22 onwards. Under that notification, the amount in excess of ₹250 was waived where the total central tax payable in the return was nil, and the amount in excess of ₹1,000 was waived for other specified taxpayers.
The example illustrates why the taxpayer must consider both Section 47 and the applicable notifications.
Section 47 and GSTR-10
Section 45 deals with the final return after cancellation of GST registration.
The final return is generally furnished in FORM GSTR-10 where applicable.
Failure to furnish the final return by its due date can attract late fee under Section 47(1).
This is particularly important for taxpayers whose GST registration has been cancelled because cancellation does not automatically remove all outstanding compliance obligations.
A taxpayer should therefore check whether GSTR-10 is required and ensure that it is filed within the applicable time.
The Government has also issued specific relief and waiver notifications for certain historical periods and forms, including GSTR-10.
Section 47 and Annual Return GSTR-9
The annual return under Section 44 is generally furnished in FORM GSTR-9 where applicable.
Delayed filing of the annual return can result in late fee under Section 47(2).
However, the effective late fee for GSTR-9 has been rationalised for specified financial years and taxpayer categories.
The GST Council has discussed a rationalised structure for annual-return late fees, including lower daily amounts and turnover-linked caps for different classes of taxpayers.
This means that a taxpayer should not simply calculate annual-return late fee by multiplying the statutory ₹100 per day by the number of delayed days without first checking the applicable notification for the relevant financial year.
Late Fee for Complete Annual Return Including GSTR-9C
An important issue arises where a taxpayer is required to furnish both:
- FORM GSTR-9; and
- FORM GSTR-9C.
CBIC issued Circular No. 246/03/2025-GST to clarify the treatment of late fee in such cases.
The circular explains that where GSTR-9C is required to be furnished along with GSTR-9, the annual return is not considered complete until both the required GSTR-9 and GSTR-9C are furnished.
The late fee under Section 47(2) is therefore calculated for the period from the due date of the annual return until the date on which the complete annual return is furnished.
This clarification is important because late fee is not separately calculated as one amount for delayed GSTR-9 and another amount for delayed GSTR-9C.
Example of Late Fee for GSTR-9 and GSTR-9C
Suppose a taxpayer is required to furnish:
- GSTR-9; and
- GSTR-9C.
The taxpayer files GSTR-9 on one date but files the required GSTR-9C later.
According to CBIC’s clarification, the annual return is treated as complete only when the required GSTR-9C is also furnished.
Therefore, the relevant period for calculating late fee under Section 47(2) can extend until the date on which the complete annual return is furnished.
Notification-Based Waiver of Late Fee
Section 47 should always be read with the Government’s power to waive late fee in appropriate circumstances.
Section 128 of the CGST Act empowers the Government, on the recommendations of the GST Council, to waive in part or in full certain penalties and late fees under Section 47 for specified classes of taxpayers and under specified mitigating circumstances.
Consequently, late fee is not always a simple fixed calculation based only on the words of Section 47.
The Government has issued various notifications providing:
- complete waiver;
- partial waiver;
- reduced daily late fee;
- maximum caps;
- conditional waiver; and
- relief for specified financial years or tax periods.
A taxpayer should therefore identify the relevant return, financial year, tax period and taxpayer category before calculating the final amount.
Example of a Late-Fee Waiver
Notification No. 08/2025-Central Tax provided a specific waiver relating to delayed furnishing of complete annual returns for financial years 2017-18 through 2022-23 for specified registered persons who were required to furnish GSTR-9C but had not furnished it along with GSTR-9 and subsequently furnished the required GSTR-9C on or before 31 March 2025.
The notification waived the late fee under Section 47 that was in excess of the amount payable up to the relevant date, subject to the conditions specified in the notification.
This was a specific historical relief and should not be treated as a general waiver applicable to all delayed annual returns.
Late Fee Is Different From Interest
Late fee and interest are two different GST liabilities.
Late Fee
Late fee is connected with delay in furnishing specified returns, statements or details.
It is governed primarily by Section 47 and relevant notifications.
Interest
Interest generally arises when tax remains unpaid or is paid late, subject to the applicable provisions of the GST law.
Therefore, a taxpayer who files a return late may potentially have both:
Late fee + interest
depending on the circumstances.
Paying the late fee does not automatically eliminate interest liability.
👉 Read More → Section 48 – Goods and services tax practitioners
Late Fee Is Different From Penalty
Late fee should also not be confused with a penalty.
Late Fee
Late fee is imposed for specified delays in furnishing returns, statements or details.
Penalty
Penalty may arise from specific contraventions under the GST Act.
A delayed return can therefore involve different consequences depending on the circumstances.
The fact that a taxpayer has paid the late fee does not necessarily mean that every other statutory consequence has been discharged.
How Is Late Fee Calculated?
The basic calculation can be understood using this formula:
Late Fee = Applicable daily late fee × Number of days of delay
However, this calculation is subject to the applicable maximum cap and any waiver, reduction or special notification.
For example, if an applicable provision results in a late fee of ₹50 per day and the delay is 10 days:
₹50 × 10 = ₹500
If a notification imposes a lower maximum cap, the final liability cannot exceed that applicable cap.
Therefore, the calculation should always follow:
Statutory provision → applicable notification → taxpayer category → return/period → number of delayed days → applicable cap
Is Late Fee Charged Per Day?
Yes, Section 47 is structured around a daily late-fee mechanism.
The statutory wording refers to late fee for every day during which the failure continues.
Therefore, the number of days of delay is an important factor.
However, the actual daily amount and maximum amount can be modified by notifications for particular returns and classes of taxpayers.
Does Late Fee Continue Until the Return Is Filed?
Generally, the statutory mechanism calculates late fee based on the period for which the filing default continues, subject to the applicable cap or waiver.
Therefore, filing the return is important not only for completing the compliance requirement but also for stopping the continuing period of delay.
The exact amount must be determined under the provisions and notifications applicable to the particular return and period.
What Is the Maximum Late Fee Under Section 47?
The answer depends on which subsection and which filing requirement is involved.
Under the statutory wording:
Section 47(1)
The statutory late fee is ₹100 per day, subject to a maximum of ₹5,000.
Section 47(2)
For the annual return under Section 44, the statutory late fee is ₹100 per day, subject to a maximum based on 0.25% of turnover in the State or Union territory.
However, these are not necessarily the final amounts payable in every practical case because notifications can reduce or waive the late fee.
Does Late Fee Apply to GSTR-1 and GSTR-3B Separately?
The treatment of different GST filings must be understood in the context of the statutory provisions and subsequent notifications.
Historically, late fee has been levied for delayed GSTR-1 and GSTR-3B filing under Section 47, with the Government later rationalising the applicable amounts through notifications.
The GST Council has also discussed the interaction between GSTR-1 and GSTR-3B, including the sequential filing requirement under Section 39(10).
Accordingly, taxpayers should not rely on a generic late-fee amount without checking the current treatment applicable to the particular return and tax period.
Can the Government Waive Late Fee?
Yes.
Section 128 gives the Government power, on the recommendations of the GST Council, to waive in part or in full any late fee referred to in Section 47 for specified classes of taxpayers and under specified mitigating circumstances.
Such waivers are generally notification-specific.
They may be:
- temporary;
- conditional;
- limited to certain tax periods;
- limited to particular forms;
- limited to particular taxpayer categories; or
- subject to a deadline for filing.
Therefore, a historical waiver should never automatically be assumed to remain available for a current period.
Can Late Fee Be Reduced by Notification?
Yes.
The Government has repeatedly rationalised late fees through notifications.
For example, Notification No. 20/2021-Central Tax rationalised the late fee for GSTR-1 by providing different caps for taxpayers based on nil outward supplies and turnover categories.
Similarly, Notification No. 21/2021-Central Tax rationalised late fee for GSTR-4.
These examples demonstrate the practical importance of checking notifications when calculating late fee.
Practical Example of Section 47
Suppose XYZ Enterprises is required to file a GST return by 20 August.
The business does not file the return by the due date and eventually files it after a delay.
The taxpayer must determine:
- which return was delayed;
- the number of days of delay;
- the statutory late-fee provision;
- the notification applicable to that return;
- whether the taxpayer falls into a special category;
- the applicable maximum cap; and
- whether any waiver is available for the relevant period.
Only after considering these factors can the correct late-fee amount be determined.
Example of Annual Return Delay
Suppose a taxpayer is required to furnish the annual return for a particular financial year.
The taxpayer misses the prescribed due date.
The taxpayer should first identify the applicable Section 47(2) provisions and the notification applicable to that financial year and taxpayer category.
If GSTR-9C is also required, the taxpayer must consider CBIC’s clarification that the annual return is complete only when the required GSTR-9 and GSTR-9C have both been furnished.
The final late-fee liability therefore depends on the applicable statutory provision, notifications and filing dates.
Section 47 and GST Compliance
Late fee is only one part of GST compliance.
A taxpayer should maintain a compliance calendar covering:
- GSTR-1;
- GSTR-3B;
- GSTR-4, where applicable;
- GSTR-9, where applicable;
- GSTR-9C, where applicable;
- GSTR-10, where applicable; and
- other applicable GST statements or returns.
The exact filing requirements depend on the taxpayer’s registration status, category, scheme and other applicable provisions.
Timely filing reduces the risk of accumulating late fees and helps maintain a clean compliance record.
What Happens If Late Fee Is Not Paid?
Where late fee is applicable, it forms part of the taxpayer’s GST compliance liability.
A taxpayer should not assume that filing the return alone necessarily settles every amount arising from delayed filing.
The applicable late fee should be discharged through the prescribed GST mechanism.
The taxpayer should also verify whether interest or any other statutory liability is separately applicable.
Common Mistakes Regarding Section 47
Mistake 1: Assuming ₹100 Per Day Always Applies
₹100 per day is the statutory amount stated in Section 47, but notifications can reduce or waive late fees for specific returns and periods.
Mistake 2: Ignoring the Maximum Cap
Late fee is subject to applicable statutory or notification-based caps.
Mistake 3: Confusing Late Fee With Interest
Late fee and interest arise for different reasons and are governed by different provisions.
Mistake 4: Assuming a Historical Waiver Is Still Available
A waiver notification normally specifies its own period, conditions and eligibility.
Mistake 5: Ignoring GSTR-9C
Where GSTR-9C is required, CBIC has clarified that the complete annual return consists of GSTR-9 together with the required GSTR-9C.
Mistake 6: Calculating Annual-Return Late Fee Without Checking Notifications
Section 47(2) provides the statutory framework, but the effective late-fee burden can be rationalised by notification.
Mistake 7: Treating Late Fee as a Penalty
Late fee is a separate statutory consequence of delayed filing and should not automatically be described as a penalty.
Section 47 and Section 46 – Difference
Section 46 and Section 47 are closely connected with return compliance, but they serve different purposes.
| Particular | Section 46 | Section 47 |
|---|---|---|
| Main subject | Notice to return defaulters | Levy of late fee |
| Purpose | Notify taxpayer about return default | Impose late fee for specified delay |
| Main mechanism | Notice under prescribed procedure | Statutory late-fee liability |
| Related form | GSTR-3A | Depends on the delayed return |
| Financial consequence | May lead to further proceedings | Late fee |
| Relationship | Deals with non-filing notice | Deals with monetary consequence of delayed filing |
A taxpayer can therefore encounter both provisions in relation to the same compliance default.
Section 47 and Section 128
Section 47 creates the late-fee framework.
Section 128 provides the Government with power to waive, in whole or in part, specified late fees under Section 47 for specified classes of taxpayers and mitigating circumstances, based on GST Council recommendations.
This relationship explains why the amount payable in a particular case may differ from the basic amount stated in Section 47.
Section 47 and Notifications
Notifications play a major practical role in determining the amount of late fee.
For example:
- Notification No. 20/2021-Central Tax rationalised late fee for GSTR-1.
- Notification No. 21/2021-Central Tax rationalised late fee for GSTR-4.
- Notification No. 08/2025-Central Tax provided specified relief relating to late fee for certain historical annual-return cases involving GSTR-9C.
These notifications demonstrate that the practical late-fee calculation must be period-specific.
Important Points to Remember
The key points regarding Section 47 are:
- Section 47 deals with the levy of late fee under the CGST Act.
- Section 47(1) covers specified details and returns.
- Section 47(2) specifically deals with the annual return under Section 44.
- The statutory wording of Section 47(1) provides ₹100 per day, subject to a maximum of ₹5,000.
- Section 47(2) provides ₹100 per day for delayed annual return, subject to the statutory turnover-linked maximum.
- These statutory amounts can be modified or waived through applicable notifications.
- GSTR-1 has been subject to notification-based rationalisation of late fee.
- GSTR-3B can attract late fee for delayed filing.
- GSTR-4 can attract late fee subject to applicable provisions and notifications.
- GSTR-10 can attract late fee when the applicable final return is filed late.
- Annual-return late fee is governed by Section 47(2) and applicable notifications.
- Where GSTR-9C is required, the complete annual return includes GSTR-9 and GSTR-9C.
- CBIC Circular No. 246/03/2025-GST clarified the calculation of late fee for delayed complete annual returns involving GSTR-9C.
- Section 128 provides the Government with power to waive specified late fees.
- Late fee is different from interest.
- Late fee is different from penalty.
- Late fee generally depends on the number of days of delay.
- Applicable caps and notification-based reductions must be considered.
- Historical waiver schemes should not automatically be applied to current tax periods.
- Taxpayers should verify the current notification applicable to the relevant return and period before calculating the final late-fee liability.
Conclusion
Section 47 of the CGST Act, 2017 provides the statutory framework for levying late fee when specified GST filing requirements are not completed within the prescribed time.
The section contains separate provisions for ordinary specified returns and details under Section 47(1) and the annual return under Section 47(2). The statutory framework provides daily late fees and applicable maximum limits, but the actual amount payable in a particular case may be reduced, capped or waived through Government notifications issued under the relevant provisions of the GST law.
This makes it important to distinguish between the basic statutory late fee and the effective late fee applicable to a particular return, taxpayer category and tax period.
Late fee can arise in connection with various GST compliance requirements, including applicable periodic returns, GSTR-4, the final return under Section 45 and the annual return under Section 44. The Government has issued several notifications over the years to rationalise late fees and provide relief for specified taxpayers and periods.
For annual returns, the position requires additional care where GSTR-9C is applicable. CBIC has clarified that the complete annual return consists of GSTR-9 together with the required GSTR-9C, and the relevant late fee is calculated with reference to the date on which the complete annual return is furnished.
In simple terms:
Section 47 creates the statutory late-fee liability, while applicable notifications determine whether the standard amount is reduced, capped or waived for a particular return, taxpayer and period.
Therefore, taxpayers should not rely only on a generic daily late-fee figure. Before making a payment, they should identify the relevant return, tax period, taxpayer category, statutory provision and current notification applicable to the case.
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