The GST Network has come out with a list of asked questions about GSTR-9 and GSTR-9C for the financial year 2024-25. This list of questions and answers is really helpful because it tells us about some changes that the GST Network is making to the system. These changes are related to how the GST Network fills in the information how it reconciles the input tax credit and how it calculates the late fee, for GST returns. The GST Network is making these changes to GSTR-9 and GSTR-9C for the year 2024-25.

These updates materially impact annual return preparation, SAP-GST reconciliation, and audit compliance. This article provides a technical breakdown of the changes and their practical implications for taxpayers and consultants.

Read full Notification - https://tutorial.gst.gov.in/downloads/news/combined_faq_on_gstr_9_and_9c_17122025.pdf

GSTR-9 & GSTR-9C Enablement Conditions (FY 2024-25)

GSTR-9 and GSTR-9C will be system-enabled only after:

• Filing of all GSTR-1 / GSTR-1A / IFF for FY 2024-25
• Filing of all GSTR-3B returns for FY 2024-25

If any return remains pending, GSTR-9 will not be enabled.

Technical Impact

This dependency ensures:

• Consistency between outward supply, ITC and tax payment data
• Elimination of partial or provisional annual returns

Auto-Population Architecture of GSTR-9 (FY 2024-25)

From FY 2024-25, the following tables of GSTR-9 are fully auto-populated:

Key Change

✔ Supplies added or amended through GSTR-1A are now included in auto-population for Tables 4 and 5.

Table 8A of GSTR-9: ITC as per GSTR-2B

Table 8A captures invoice-level ITC data for FY 2024-25 based on GSTR-2B.

Inclusion Criteria

• Invoices pertaining to FY 2024-25 appearing in GSTR-2B
• Invoices of FY 2024-25 reflected in GSTR-2B of April–October 2025
• Excludes FY 2023-24 invoices reflected late

IMS Dashboard Clarification

Actions taken in IMS (Invoice Management System) do not directly affect GSTR-9.

Only accepted or deemed-accepted documents appearing in GSTR-2B are considered.

Table 8A Excel vs Table 8A Online – Reconciliation Perspective

GSTN has clarified that differences between Table 8A Excel and Online view are expected.

Causes of Differences

• RCM outward supplies
• Cross-FY invoice amendments
• Place of Supply corrections
• ITC eligibility changes

Compliance Guidance

✔ Table 8A Online is final for GSTR-9

✔ Excel file is a diagnostic and reconciliation tool only

Introduction of Table 6A1 – Segregation of Prior-Year ITC

What Table 6A1 Captures

• ITC pertaining to FY 2023-24 claimed in FY 2024-25
• Excludes ITC reclaimed under Rule 37 / 37A

Formula Impact

Table 6A2 = Table 6A – Table 6A1

System Benefit

• Eliminates artificial mismatches in Table 6J
• Aligns annual return logic with ITC year attribution principles

ITC Claim, Reversal & Reclaim – Rule-Based Reporting Framework

Same FY Claim-Reversal-Reclaim

Reclaim in Subsequent FY

• Rule 37 / 37A → ITC belongs to year of reclaim
• Other reasons → Report in Table 13 + next year 6A1

Table 8B, 8C & 8D – Revised Auto-Population Logic

Major System Change

• Table 8B auto-populates only from Table 6B
• Table 6H is delinked from Table 8B

Outcome

✔ Reclaimed ITC does not inflate differences

✔ Table 8D mismatches significantly reduced

New Table 8H1 – Import ITC Claimed in Next FY

Scenario

• Goods imported in FY 2024-25
• ITC availed in FY 2025-26

Reporting Structure

Tax Payable Reporting in Table 9 – Negative Liability Handling

• Table 9 auto-populates from net tax liability in GSTR-3B
• If liability is negative, no value is auto-filled
• Table remains editable

GSTR-9C Late Fee Computation – FY 2024-25

As per Circular 246/03/2025-GST:

• Late fee under Section 47(2) applies to GSTR-9 and GSTR-9C
• New Table 17 added in GSTR-9C

Late Fee Calculation

• GSTR-9 → Due date till filing
• GSTR-9C → Filing of GSTR-9 (or due date) till filing of 9C
• Late fee is system-computed

HSN Reporting Enhancement in GSTR-9

GSTN has provided:

• Download Table 12 of GSTR-1/1A (Excel)
• Additional HSN-wise sheet aligned with Table 17 of GSTR-9

This improves HSN accuracy and audit traceability.

Other Important Technical Clarifications

• ❌ 65% concessional tax rate removed from Tables 17 & 18
• ❌ Non-GST purchases not reportable in GSTR-9
• 🛒 Table 4G1 applicable only to e-commerce operators u/s 9(5)
• 🔁 RCM paid in FY 2025-26 → Report in GSTR-9 of FY 2025-26

Conclusion: Compliance & System Readiness for FY 2024-25

The FY 2024-25 GSTR-9 & 9C framework introduces:

• Stronger system validations
• Clear ITC year segregation
• Reduced reconciliation mismatches

However, taxpayers must ensure:

✔ Accurate GSTR-2B reconciliation

✔ Correct ITC year classification

✔ Timely filing to avoid late fees

Automated GST reconciliation, SAP-based GST cockpits, and rule-driven ITC engines are now essential to ensure compliant and error-free annual return filing.