GSTR-9/ 9C Late Fee Calculation Guide for FY 2024-25

Late fee provisions for annual returns underwent significant clarification through Circular No. 246/03/2025-GST dated January 30, 2025, fundamentally changing how we understand penalties for delayed GSTR-9 and GSTR-9C filing. The critical revelation: late fee under Section 47(2) applies to the complete annual return, which includes both GSTR-9 and GSTR-9C (where applicable).

This means late fees aren’t calculated separately for each form, they’re calculated as a continuous obligation from the due date until you complete your entire annual return filing. For FY 2024-25, understanding this integrated late fee calculation, the new Table 17 in GSTR-9C, and the system’s auto-calculation logic is essential for accurate compliance and avoiding surprises at the time of filing.

This blog post explains due dates, late fee calculation methodology, system auto-calculation mechanics, and provides detailed examples covering various filing scenarios.

Due Dates for GSTR-9 and GSTR-9C FY 2024-25

Standard Due Dates

GSTR-9 (Annual Return): December 31, 2025
GSTR-9C (Reconciliation Statement): December 31, 2025

Both forms have the same due date, reinforcing the concept that they’re components of a single “complete annual return” obligation.

Who Must File GSTR-9?

All registered taxpayers (except certain exempt categories like composition dealers, ISD, OIDAR service providers, non-resident taxable persons, and casual taxable persons) must file GSTR-9 if they were registered during FY 2024-25.

Who Must File GSTR-9C?

Taxpayers whose aggregate turnover during FY 2024-25 exceeds:

• ₹5 crores: Previous threshold (applicable till FY 2023-24)
• ₹10 crores: New threshold from FY 2024-25 onwards (as per recent amendments)

Note: Verify the applicable threshold based on latest notifications at the time of filing.

GSTR-9C must be certified by a Chartered Accountant or Cost Accountant.

Section 47(2): The Legal Foundation

Section 47(2) of the CGST Act provides:

“Any registered person who fails to furnish the details of outward or inward supplies required under section 37 or section 38 or returns required under section 39 or section 45 by the due date shall pay a late fee of one hundred rupees for every day during which such failure continues subject to a maximum amount of five thousand rupees.”

For annual returns, this translates to:

• ₹100 per day of delay (₹50 CGST + ₹50 SGST)
• Maximum ₹5,000 (₹2,500 CGST + ₹2,500 SGST)

The Circular 246/03/2025-GST Clarification: Game Changer

What the Circular Clarified

The January 30, 2025 circular made explicit what was previously ambiguous:

“Late fee is levied under Section 47(2) of the CGST Act for any delay in furnishing the complete annual return under Section 44. This includes both FORM GSTR-9 and FORM GSTR-9C (if applicable).”

What This Means in Practice

The annual return obligation under Section 44 is considered incomplete until:

• GSTR-9 is filed, AND
• GSTR-9C is also filed (if you’re liable to file it based on turnover)

Late fee accrues continuously from the due date until you complete both filings.

The Two-Stage Late Fee Calculation

Following this clarification, GSTR-9C introduces Table 17: “Late Fee Payable and Paid” to capture the bifurcated late fee:

Stage 1: Due date to GSTR-9 filing (or due date, whichever is later)
Stage 2: GSTR-9 filing date (or due date, whichever is later) to GSTR-9C filing

This bifurcation ensures:

• Late fee for Stage 1 is paid when filing GSTR-9
• Late fee for Stage 2 is paid when filing GSTR-9C
• Together, they represent the total late fee for delayed complete annual return

How the System Auto-Calculates Late Fee

Both GSTR-9 and GSTR-9C have system auto-calculation of late fees based on filing dates.

For GSTR-9

Calculation starts: December 31, 2025 (due date)
Calculation ends: Date you actually file GSTR-9
Days counted: Calendar days (not working days)

Formula:

• If filed on or before December 31, 2025: ₹0
• If filed after December 31, 2025: (Number of days delayed × ₹100) subject to maximum ₹5,000

System Behavior:

• Late fee auto-populates when you attempt to file
• You must pay before submission
• Payment integrated into filing process

For GSTR-9C (New Table 17)

Calculation starts:

• If GSTR-9 filed after due date: Date of GSTR-9 filing
• If GSTR-9 filed on or before due date: Due date (December 31, 2025)

Calculation ends: Date you actually file GSTR-9C

Formula:

• Days between start date and GSTR-9C filing × ₹100
• Subject to maximum ₹5,000

Key Point: If GSTR-9 already accumulated some late fee (filed late), GSTR-9C only calculates additional days from GSTR-9 filing to GSTR-9C filing.

Detailed Examples: Late Fee Calculation Scenarios

Let’s work through comprehensive examples covering different filing timings.

Example 1: Both Filed Within Due Date (No Late Fee)

Facts:

• GSTR-9 filed: December 25, 2025
• GSTR-9C filed: December 30, 2025
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Filed before due date
• Late fee: ₹0

GSTR-9C Table 17:

• GSTR-9 was filed on time, so count from due date (December 31, 2025)
• But GSTR-9C filed before due date (December 30, 2025)
• Late fee: ₹0

Total Late Fee: ₹0

Takeaway: File both before due date to avoid any late fee.

Example 2: GSTR-9 on Time, GSTR-9C Delayed

Facts:

• GSTR-9 filed: December 25, 2025
• GSTR-9C filed: January 7, 2026
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Filed before due date
• Late fee: ₹0

GSTR-9C Table 17:

• GSTR-9 filed on time, so count from due date (December 31, 2025)
• GSTR-9C filed: January 7, 2026
• Days delayed: January 1 to January 7 = 7 days
• Late fee: 7 days × ₹100 = ₹700

Total Late Fee: ₹700 (all paid at GSTR-9C filing)

System Behavior:

• No late fee demanded when filing GSTR-9 on December 25
• ₹700 auto-populated in GSTR-9C Table 17 when filing on January 7

Example 3: GSTR-9 Delayed, GSTR-9C on Same Day

Facts:

• GSTR-9 filed: January 5, 2026
• GSTR-9C filed: January 5, 2026 (same day)
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Due date: December 31, 2025
• Filed: January 5, 2026
• Days delayed: January 1 to January 5 = 5 days
• Late fee: 5 days × ₹100 = ₹500

GSTR-9C Table 17:

• GSTR-9 filed on January 5, 2026
• GSTR-9C also filed on January 5, 2026 (same day)
• Days delayed: 0 days (no additional delay beyond GSTR-9 delay)
• Late fee: ₹0

Total Late Fee: ₹500 (all paid at GSTR-9 filing)

Takeaway: If you’re late, filing GSTR-9C immediately after GSTR-9 prevents additional late fee accumulation.

Example 4: Both Delayed, Filed on Different Days (The Standard Case)

Facts:

• GSTR-9 filed: January 5, 2026
• GSTR-9C filed: January 7, 2026
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Due date: December 31, 2025
• Filed: January 5, 2026
• Days delayed: January 1 to January 5 = 5 days
• Late fee at GSTR-9 filing: 5 days × ₹100 = ₹500

GSTR-9C Table 17:

• GSTR-9 filed: January 5, 2026
• GSTR-9C filed: January 7, 2026
• Additional days: January 6 to January 7 = 2 days
• Late fee at GSTR-9C filing: 2 days × ₹100 = ₹200

Total Late Fee: ₹500 (GSTR-9) + ₹200 (GSTR-9C) = ₹700

Breakdown by Form:

• Paid with GSTR-9: ₹500
• Paid with GSTR-9C: ₹200

System Behavior:

• January 5: System demands ₹500 when filing GSTR-9
• January 7: System auto-populates ₹200 in GSTR-9C Table 17

Example 5: Long Delay with Maximum Late Fee Cap

Facts:

• GSTR-9 filed: March 15, 2026
• GSTR-9C filed: March 20, 2026
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Due date: December 31, 2025
• Filed: March 15, 2026
• Days delayed: January 1 to March 15 = 74 days
• Calculated late fee: 74 days × ₹100 = ₹7,400
• But maximum is ₹5,000
• Late fee at GSTR-9 filing: ₹5,000

GSTR-9C Table 17:

• GSTR-9 filed: March 15, 2026 (already hit maximum)
• GSTR-9C filed: March 20, 2026
• Additional days: March 16 to March 20 = 5 days
• Calculated late fee: 5 days × ₹100 = ₹500
• Total late fee if no cap: ₹5,000 + ₹500 = ₹5,500
• But maximum total is ₹5,000
• Since ₹5,000 already paid at GSTR-9, GSTR-9C late fee: ₹0

Total Late Fee: ₹5,000 (all paid at GSTR-9 filing; GSTR-9C adds nothing more)

Critical Point: The ₹5,000 maximum applies to the total combined late fee for complete annual return, not separately to each form.

Example 6: GSTR-9 Near Maximum, GSTR-9C Pushes Over

Facts:

• GSTR-9 filed: February 18, 2026
• GSTR-9C filed: February 25, 2026
• Due date: December 31, 2025

Late Fee Calculation:

GSTR-9:

• Days delayed: January 1 to February 18 = 49 days
• Calculated late fee: 49 days × ₹100 = ₹4,900
• Within maximum: ₹4,900

GSTR-9C Table 17:

• Additional days: February 19 to February 25 = 7 days
• Calculated late fee: 7 days × ₹100 = ₹700
• Combined total: ₹4,900 + ₹700 = ₹5,600
• But maximum total is ₹5,000
• Amount already paid: ₹4,900
• Remaining before cap: ₹5,000 – ₹4,900 = ₹100
• GSTR-9C late fee: ₹100 (not full ₹700)

Total Late Fee: ₹4,900 (GSTR-9) + ₹100 (GSTR-9C) = ₹5,000 (capped)

System Behavior: GSTR-9C Table 17 auto-calculates ₹100, recognizing the maximum cap has been reached.

Example 7: GSTR-9 After Due Date but Before Year-End

Facts:

• Due date: December 31, 2025
• GSTR-9 filed: December 31, 2025 (on due date but late in the day, technically after midnight, system treats as filed)
• GSTR-9C filed: January 10, 2026

Late Fee Calculation:

GSTR-9:

• Filed on due date
• Late fee: ₹0

GSTR-9C Table 17:

• Start counting: January 1, 2026 (day after due date, since GSTR-9 filed on due date)
• GSTR-9C filed: January 10, 2026
• Days: January 1 to January 10 = 10 days
• Late fee: 10 days × ₹100 = ₹1,000

Total Late Fee: ₹1,000

Practical Tip: If you can only file GSTR-9 on December 31, make sure it’s successfully filed (not just uploaded) before midnight to avoid starting the late fee clock.

The Date Counting Logic

Understanding exactly how days are counted is crucial for verification:

Inclusive or Exclusive Counting?

First day (day after due date or GSTR-9 filing): Included in count
Last day (day of GSTR-9C filing): Included in count

Example:

• Due date: December 31, 2025
• Filed: January 3, 2026

Day 1: January 1, 2026
Day 2: January 2, 2026
Day 3: January 3, 2026

Total: 3 days × ₹100 = ₹300

How to Calculate Days Between Dates

Formula: (Filing Date – Due Date) = Number of Days

Example:

• Due date: December 31, 2025
• Filing date: January 15, 2026
• Calculation: January 15 – December 31 = 15 days

Or count: January 1, 2, 3, …, 15 = 15 days

Month-End and Month-Start Considerations

Scenario: Due date December 31, filed January 1 (next day)

• Only 1 day late
• Late fee: ₹100

Don’t count December 31 itself (that’s the due date, not a delay day).

GSTR-9C Table 17: Structure and Auto-Population

The new Table 17 in GSTR-9C for FY 2024-25 has the following structure:

Table 17 Fields

17A: Late fee payable (auto-calculated by system)
17B: Late fee paid (system-populated after payment)

Both have sub-fields for:

• Central Tax (CGST)
• State Tax (SGST) / UT Tax (UTGST)
• Integrated Tax (IGST) – typically ₹0 for late fees

Auto-Population Logic

When you open GSTR-9C for filing, the system:

1. Checks GSTR-9 filing date: Retrieves the date you filed GSTR-9 for FY 2024-25
2. Determines start date for GSTR-9C late fee:
   • If GSTR-9 filed on or before December 31, 2025: Start = January 1, 2026
   • If GSTR-9 filed after December 31, 2025: Start = Day after GSTR-9 filing
3. Checks current date: When you attempt to file GSTR-9C
4. Calculates days: Current date – Start date
5. Applies rate: Days × ₹100 (₹50 CGST + ₹50 SGST)
6. Applies cap: Checks if GSTR-9 late fee + GSTR-9C late fee exceeds ₹5,000; if so, caps the total
7. Auto-populates Table 17A: Displays the calculated late fee amount

Payment Integration

After Table 17A shows the auto-calculated late fee:

1. You must pay the amount through the GST portal payment mechanism
2. Payment creates a challan with unique identification
3. After successful payment, Table 17B auto-populates with paid amount
4. Only after payment confirmation can you submit GSTR-9C
5. System validates that 17B equals 17A before allowing submission

What If You Disagree with Auto-Calculated Amount?

Short answer: You cannot manually edit the late fee amount in Table 17.

If you believe calculation is wrong:

• Verify GSTR-9 filing date in system records
• Check date calculation manually
• If system error confirmed, raise grievance through GST portal
• Pay the auto-calculated amount to file (to avoid further delay)
• Claim refund later if grievance establishes system error

Practical reality: System calculations are generally accurate. Most “disagreements” stem from misunderstanding the counting methodology or the date GSTR-9 was actually filed (vs. when you thought you filed it).

Strategic Considerations: When to File What

Understanding late fee calculation creates strategic filing decisions:

Strategy 1: File Both Together (Minimize Total Late Fee)

Scenario: You’re already past due date.

Best Practice: Complete GSTR-9, immediately prepare and file GSTR-9C on the same day.

Benefit:

• Only one set of daily late fees (through GSTR-9 filing)
• Zero additional late fee for GSTR-9C
• Total late fee minimized

Example:

• Both filed January 10, 2026
• Late fee: 10 days × ₹100 = ₹1,000 (all paid with GSTR-9)
• GSTR-9C late fee: ₹0

Strategy 2: File GSTR-9 First, Gather GSTR-9C Data Later

Scenario: GSTR-9 data is ready, but GSTR-9C requires auditor certification and additional reconciliation work.

Approach: File GSTR-9 first to stop the clock, complete GSTR-9C later.

Cost: Additional late fee for days between GSTR-9 and GSTR-9C filing.

Example:

• GSTR-9 filed: January 10, 2026 (late fee: ₹1,000)
• GSTR-9C requires 10 more days for auditor certification
• GSTR-9C filed: January 20, 2026 (additional late fee: ₹1,000)
• Total late fee: ₹2,000

When to use: When GSTR-9C delay would significantly exceed GSTR-9 completion time, and you want to cap at least part of the late fee.

Strategy 3: Wait for Both to Be Complete

Scenario: Neither form is ready by due date.

Approach: Work on both simultaneously, file both when ready.

Risk: If one form finishes earlier but you wait for the other, you’re accruing unnecessary late fee for the completed form.

Best Practice: File GSTR-9 as soon as ready (stops clock for first stage), then rush GSTR-9C.

Strategy 4: Strategic Timing Near Maximum

Scenario: You’re approaching the ₹5,000 maximum late fee cap.

Calculation: 50 days × ₹100 = ₹5,000 (maximum reached)

Strategic Point: If already delayed 50+ days, there’s no additional financial penalty for further delay (you’ve hit the cap).

Ethical Note: While financially there’s no additional cost after 50 days, continued non-compliance may trigger other enforcement actions (notices, assessments, etc.). The cap is a penalty ceiling, not a license for indefinite delay.

Interest vs. Late Fee: Important Distinction

Late fee under Section 47(2) is not the same as interest under Section 50.

Late Fee (Section 47(2))

• For late filing of returns
• Flat ₹100 per day (up to ₹5,000 max)
• Applies regardless of tax liability

Interest (Section 50)

• For late payment of tax
• 18% per annum on unpaid tax amount
• Calculated from due date of payment to actual payment date
• No maximum cap

Both Can Apply Simultaneously

Scenario: You have tax liability in FY 2024-25, file annual return late, and haven’t paid some tax.

You owe:

1. Late fee: For delayed GSTR-9/9C filing (₹100/day up to ₹5,000)
2. Interest: On unpaid tax amount (18% p.a., no cap)

Example:

• Tax liability: ₹1,00,000 (unpaid)
• Due date for payment and annual return: December 31, 2025
• GSTR-9 filed: February 15, 2026 (46 days late)
• GSTR-9C filed: February 20, 2026 (51 days late)

Late Fee Calculation:

• 51 days × ₹100 = ₹5,100, but capped at ₹5,000

Interest Calculation (on ₹1,00,000 unpaid tax):

• December 31, 2025 to February 20, 2026 = 51 days
• Interest: ₹1,00,000 × 18% × (51/365) = ₹2,516

Total Amount Due: ₹5,000 (late fee) + ₹2,516 (interest) = ₹7,516 (plus the original ₹1,00,000 tax)

Nil Return and Late Fee

Question: If I have nil liability for the year, do I still pay late fee for delayed GSTR-9 filing?

Answer: Yes. Late fee under Section 47(2) is for delay in filing, not related to whether you have tax liability.

Reasoning: The annual return serves statutory compliance and transparency purposes beyond just tax payment. Even with nil liability, you must file on time or incur late fee.

Example:

• FY 2024-25: No business activity, nil ITC, nil outward supplies
• GSTR-9 shows zeros across all tables
• But you file on January 20, 2026 (20 days late)
• Late fee: 20 days × ₹100 = ₹2,000 (still applicable)

Common Scenarios and Clarifications

Scenario 1: Filed GSTR-9, Forgot About GSTR-9C

Facts:

• Turnover: ₹12 crores (GSTR-9C applicable)
• GSTR-9 filed: December 28, 2025 (on time)
• Forgot about GSTR-9C until February 10, 2026

Late Fee:

• GSTR-9: ₹0 (filed on time)
• GSTR-9C: January 1 to February 10 = 41 days
• Late fee: 41 days × ₹100 = ₹4,100

Learning: Even if GSTR-9 filed on time, forgetting GSTR-9C (when applicable) triggers late fee from January 1.

Scenario 2: Turnover Uncertainty and GSTR-9C

Facts:

• Estimated turnover: ₹9.8 crores (thought GSTR-9C not needed)
• Filed only GSTR-9 on December 30, 2025
• March 2026: Finalized accounts show turnover ₹10.2 crores (GSTR-9C needed)
• File GSTR-9C: March 15, 2026

Late Fee:

• GSTR-9: ₹0 (filed on time)
• GSTR-9C: Should have been filed by December 31, 2025
• Start counting: January 1, 2026 (from due date, not GSTR-9 filing)
• Days: January 1 to March 15 = 74 days
• Calculated: 74 × ₹100 = ₹7,400
• Capped at: ₹5,000

Practical Tip: If turnover is borderline, prepare GSTR-9C proactively. Better to have it ready and not need it than discover liability later.

Scenario 3: Multiple Revisions

Question: If I file GSTR-9 late, pay late fee, then revise GSTR-9, do I pay late fee again?

Answer: No. Late fee is charged once for the original delayed filing. Revisions (if permitted) don’t attract additional late fee.

Clarification: As of current rules, GSTR-9 generally cannot be revised. But if the facility becomes available and you revise:

• Original late fee already paid (based on first filing date)
• Revision filing doesn’t restart late fee clock
• However, interest on any additional tax discovered may apply

Scenario 4: Filed Wrong Form By Mistake

Facts:

• Turnover ₹12 crores (both GSTR-9 and GSTR-9C needed)
• December 30, 2025: Filed GSTR-9 (thinking done)
• January 15, 2026: Realized GSTR-9C also needed
• File GSTR-9C: January 15, 2026

Late Fee:

• GSTR-9: ₹0 (filed on time)
• GSTR-9C: January 1 to January 15 = 15 days
• Late fee: 15 × ₹100 = ₹1,500

No Waiver for Mistake: Ignorance or mistake doesn’t waive late fee. You’re expected to know your obligations based on turnover.

Scenario 5: System Downtime on Due Date

Question: If GST portal is down on December 31, 2025 and I cannot file, am I liable for late fee?

Answer: Typically, if system issues prevent filing on due date, government extends the deadline through notification.

Best Practice:

• Don’t wait until last day to file
• If system down on due date, immediately file grievance
• Take screenshots of error messages
• File as soon as system restored
• If extension granted, original late fee calculation may be modified

Note: Extensions are discretionary and must be officially notified. Absent notification, late fee applies.

How to Verify Late Fee Calculation

When system shows late fee at time of filing, verify:

Step 1: Confirm Due Date

• Standard: December 31, 2025
• Check for any official extensions through notifications

Step 2: Confirm GSTR-9 Filing Date

• Go to: Returns → Filed Returns
• Find: GSTR-9 for FY 2024-25
• Note: Date of filing (not date of generation or download)

Step 3: Calculate Days for GSTR-9 Late Fee

• If GSTR-9 filed after December 31, 2025:
• Days = (GSTR-9 Filing Date – December 31, 2025)
• Expected late fee = Days × ₹100 (capped at ₹5,000)

Step 4: Calculate Days for GSTR-9C Late Fee (When Filing GSTR-9C)

• If GSTR-9 filed on or before December 31, 2025:
  • Start = January 1, 2026
• If GSTR-9 filed after December 31, 2025:
  • Start = Day after GSTR-9 filing date
• Days = (Current GSTR-9C Filing Date – Start Date)
• Expected late fee = Days × ₹100, adjusted for maximum cap

Step 5: Check Maximum Cap Applicability

• Total combined late fee (GSTR-9 + GSTR-9C) cannot exceed ₹5,000
• If GSTR-9 late fee was ₹4,500, GSTR-9C can only add ₹500 more

Step 6: Compare with System Calculation

• If matches: Proceed with payment
• If differs significantly: Raise query before paying

Best Practices to Minimize Late Fee

1. File Well Before Due Date

Target: Complete filing by mid-December 2025

Benefits:

• Zero late fee risk
• Time to address any last-minute issues
• Reduced year-end compliance burden

Process:

• September 2025: Begin data compilation
• October 2025: Complete internal reconciliation
• November 2025: Prepare GSTR-9 and GSTR-9C (if applicable)
• December 1-15, 2025: Review and file

2. Enable GSTR-9 Early

Ensure all GSTR-1 and GSTR-3B for FY 2024-25 are filed by October 2025, enabling GSTR-9 to be accessible.

Benefit: More time to review auto-populated data and make necessary corrections.

3. Coordinate with Auditor Early (for GSTR-9C)

If GSTR-9C applicable:

• Engage CA/CMA by September 2025
• Provide books and data by October 2025
• Target audit completion by November 2025
• File GSTR-9 and GSTR-9C together in December

Avoids: Situation where GSTR-9 is ready but waiting for auditor delays GSTR-9C.

4. Set Internal Deadlines

Internal target: December 15, 2025 (16 days before due date)

Buffer: Provides cushion for:

• Technical issues
• Last-minute data corrections
• Auditor queries
• Unforeseen circumstances

5. Monitor Official Notifications

Check GST portal regularly for:

• Due date extensions (rare but possible)
• Changes in late fee provisions
• Technical advisory about portal maintenance

6. Use Reminders and Checklists

System reminders:

• November 1, 2025: “GSTR-9 due in 60 days”
• December 1, 2025: “GSTR-9 due in 30 days”
• December 15, 2025: “GSTR-9 due in 16 days – FILE NOW”

Checklist:

• All GSTR-1 filed for FY 2024-25
• All GSTR-3B filed for FY 2024-25
• GSTR-9 enabled on portal
• Reconciliation completed
• GSTR-9 prepared and reviewed
• GSTR-9C (if applicable) prepared
• Auditor certification obtained
• Both forms filed
• Acknowledgments downloaded

Late Fee Payment Process

Step 1: Attempt to Submit Return

When you click “Submit” in GSTR-9 or “File” in GSTR-9C, system calculates late fee.

Step 2: Late Fee Display

System shows:

• Number of days delayed
• Calculated late fee (CGST, SGST breakup)
• “Pay Now” option

Step 3: Make Payment

Click “Pay Now” → Redirects to payment interface

Payment options:

• Electronic Cash Ledger (if sufficient balance)
• Create new challan (internet banking, debit card, NEFT/RTGS)

Step 4: Payment Confirmation

After successful payment:

• Challan generated with CIN (Challan Identification Number)
• Amount reflects in Electronic Cash Ledger
• System links payment to pending late fee obligation

Step 5: Complete Filing

Return to GSTR-9 or GSTR-9C filing screen:

• Late fee now shows as “Paid”
• “Submit” or “File” button becomes active
• Complete submission

Step 6: Download Acknowledgment

• After successful filing, download acknowledgment
• Retain for records along with payment challan

What If You Cannot Pay Late Fee?

Short answer: You cannot file the return without paying late fee.

Options if facing financial difficulty:

1. Partial Payment Not Allowed: System requires full late fee payment; you cannot pay partially and complete filing later.
2. No Installment Option: Unlike tax liability (which can sometimes be paid in installments under schemes), late fee must be paid in full.
3. No Waiver Provision: Currently, there’s no provision for waiver of late fee based on financial hardship.
4. Only Option: Arrange funds and pay the late fee to complete filing.
5. Continued Delay Costs: Every additional day of delay adds ₹100 late fee (until ₹5,000 cap), so prolonging doesn’t help.

Practical Advice: If late fee has reached ₹5,000 cap (50 days delay), you have no additional financial penalty for further delay in filing. However:

• Non-filing remains a compliance violation
• May attract notices and scrutiny
• Other enforcement actions possible
• Better to file even after long delay than not file at all

Record Keeping for Late Fee

Maintain the following documentation:

1. Filing Date Proof

• GSTR-9 acknowledgment with date and time stamp
• GSTR-9C acknowledgment with date and time stamp

2. Payment Proof

• Late fee payment challan(s)
• Bank statement showing debit
• Electronic Cash Ledger statement showing credit and utilization

3. Calculation Worksheet

• Manual calculation of expected late fee
• Comparison with system-calculated amount
• Notes on any discrepancies

4. Correspondence

• Any portal grievances raised about late fee calculation
• Responses received from authorities
• Screenshots if system errors encountered

5. Extension Notifications (if any)

• Official notifications extending due dates
• Applicability confirmation for your category

Retention Period: Maintain for at least 6 years from end of FY (as required for GST records generally).

Conclusion

Late fee calculation for GSTR-9 and GSTR-9C under Section 47(2) follows a clear methodology: ₹100 per day of delay, capped at ₹5,000 total for the complete annual return. The critical insight from Circular 246/03/2025-GST is that GSTR-9 and GSTR-9C together constitute the “complete annual return,” with late fee accruing continuously from due date until both forms are filed (where applicable).

Key takeaways for FY 2024-25:

1. Due date: December 31, 2025 for both GSTR-9 and GSTR-9C
2. System auto-calculates: Late fee based on actual filing dates
3. Two-stage payment: GSTR-9 filing triggers first late fee; GSTR-9C triggers additional late fee for any gap
4. Maximum cap: ₹5,000 combined for both forms
5. Strategic filing: File GSTR-9 and GSTR-9C together when delayed to minimize additional late fee

By understanding the calculation methodology, planning for timely filing, and using the strategic insights in this guide, you can either avoid late fees entirely or minimize them when delays are unavoidable. Remember: late fee is for non-filing; interest is for non-payment; both may apply simultaneously if you have tax liability.

Final article Next in series: HSN reporting, Table 17/18 changes, label updates, and practical tips for using offline tools and download templates for efficient GSTR-9 completion.

Reference:

GSTN’s Consolidated FAǪs on GSTR 9/9C for the FY 2024-25 dated 17/12/2025