The "Amnesty Scheme" discussed in your forum post refers to a specific, time-bound relief program from 2021 designed to help taxpayers regularize pending GSTR-3B filings by capping late fees.
Context of the 2021 Amnesty Scheme
The scheme you are inquiring about, which was active from June 1, 2021, to November 30, 2021, allowed for reduced late fees for GSTR-3B returns that were pending for the period between July 2017 and April 2021.
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For Nil Returns: The maximum late fee was capped at ₹500 (₹250 CGST + ₹250 SGST) per return.
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For Non-Nil Returns: The maximum late fee was capped at ₹1,000 (₹500 CGST + ₹500 SGST) per return.
Why Your Portal May Still Show High Fees
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Scheme Expiry: The amnesty period for these specific returns ended on November 30, 2021. If you are attempting to file those old returns now (in 2026), the system will likely revert to standard late fee calculations (which are much higher and subject to daily accrual) because the amnesty window has long since passed.
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Automatic Application: During the active window, the benefit was generally applied automatically by the system upon filing. It did not require a separate manual application, but it did require the filing to be completed within the notified deadline.
Recommended Steps
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Verify the Period: Ensure the returns you are filing are indeed within the scope of the original amnesty. If you are filing returns for periods after April 2021, those do not qualify for the 2021 amnesty.
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Consult a Professional: Since the 2021 scheme is closed, you should consult with a tax professional or your jurisdictional GST officer to understand if there are any current measures or legal pathways available to settle your specific outstanding dues for that period.
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Avoid Misconception: Be aware that "Amnesty Schemes" are introduced by the government as specific, non-permanent notifications. Any new notifications or amnesty-like benefits (such as the recent Section 128A waiver for certain Section 73 demands) have different eligibility criteria, timelines, and procedures.
Summary: The 2021 GST Amnesty Scheme, which provided the capped late fees of ₹500/₹1,000 for pending 2017–2021 returns, concluded on November 30, 2021. You cannot avail of these specific capped rates for filings made today. You should check with a tax expert regarding current options for resolving long-pending returns.