GSTR-9 & GSTR-9C Difficulties: Common Filing Issues and Solutions

GSTR‑9 & GSTR‑9C difficulties usually surface only at year‑end, when reconciliations, data gaps and portal issues collide with tight timelines. This article walks through the typical pain points and practical fixes to help teams close GST annual compliance with fewer surprises.

Key Takeaways

• GSTR‑9 is an informational annual return that consolidates data from all GST returns for the year, whereas GSTR‑9C is an analytical reconciliation statement between audited financials and GSTR‑9, self‑certified by the CFO/finance head for eligible taxpayers.
• Most challenges arise due to insufficient reconciliations between GSTR‑1, GSTR‑3B, GSTR‑2B and books of account, especially for turnover, tax and ITC.
• Technical glitches, JSON errors and last‑minute corrections in books or returns significantly increase the risk of mismatches, notices and additional tax demand.
• A structured pre‑filing checklist, early reconciliations and use of automation tools can sharply reduce GSTR‑9 & GSTR‑9C filing difficulties.

What are the GST Annual Returns

GST annual returns are yearly statements that summarise all outward supplies, inward supplies, ITC and tax payments made during a financial year across periodic returns. They provide the administration a high‑level, year‑end view of a taxpayer’s compliance and help flag inconsistencies in reporting.

• GSTR‑9: Annual return to be filed for each registration (GSTIN) by regular taxpayers above the notified turnover threshold (currently INR 2 crore for many recent years).
• GSTR‑9C: Self‑certified reconciliation statement for taxpayers with turnover exceeding INR 5 crore, comparing audited financials with figures declared in GSTR‑9.

Common Difficulties in GSTR‑9 Filing

GSTR‑9 & GSTR‑9C difficulties often start with GSTR‑9, which aggregates the entire year’s data, including all corrections and amendments.

Typical GSTR‑9 Pain Points

• Reconciliation gaps with GSTR‑1, 3B and books
  • Turnover as per GSTR‑1 may not match GSTR‑3B or financial statements due to timing differences, missed amendments, and credit notes issued late.
  • ITC reported in GSTR‑2A/2B may not align with ITC booked in books or claimed in GSTR‑3B, especially where vendors filed returns late or incorrectly.
• Granular classification and table‑wise mapping
  • Taxpayers struggle to split ITC into inputs, input services and capital goods and to segregate current‑year vs prior‑year ITC in revised tables such as 6A1.
  • Reverse charge liability and corresponding ITC often get misreported between years, despite CBIC clarifications that RCM should be reported in the year of payment.
• Historic amendments and exemptions
  • Multiple relaxations, optional tables for earlier years, and changes in instructions over FY 2017‑18 to 2022‑23 have created confusion about what exactly needs to be reported.
  • Taxpayers close to the ₹2 crore threshold often mis‑read exemption notifications and either skip GSTR‑9 or file it unnecessarily.

Common Difficulties in GSTR‑9C Filing

GSTR‑9C is where many CFOs feel the pressure, because any mismatch between books and GST returns gets formally documented and self‑certified.

GSTR‑9C Challenges in Practice

• Turnover and tax reconciliation
  • Differences between audited financial turnover and GSTR‑9 turnover arise from non‑GST revenue, branch transfers, or revenue recognised but not yet invoiced.
  • Under‑ or over‑statement of tax liability in GSTR‑3B, when compared to the tax payable as per books, leads to adjustments and disclosure of additional liability in GSTR‑9C.
• ITC reconciliation complexity
  • ITC in books, GSTR‑3B and GSTR‑2B rarely match perfectly, forcing line‑by‑line reconciliations across thousands of invoices in larger organisations.
  • Ineligible credits (blocked credits, non‑business expenses, time‑barred ITC) are sometimes not filtered out correctly before filing, triggering audit qualifications.
• Technical and format‑related issues
  • Uploading JSON files often throws “mismatch in data” or validation errors where GSTR‑9C values do not match GSTR‑3B/9 or schema expectations.
  • Version changes in the utility close to the due date have historically created last‑minute re‑work for preparers and reviewers.

Frequent Errors That Trigger GST Notices

Many GSTR‑9 & GSTR‑9C difficulties translate into scrutiny notices, DRC‑01 intimation or selection for audit/special investigation.

High‑Risk Errors and Mismatches

A GST analytics study by the administration indicated that mismatches in ITC between GSTR‑3B and GSTR‑2A/2B are among the top triggers for automated notices.

Practical Solutions for GSTR‑9 & 9C Filing Difficulties

GSTR‑9 & GSTR‑9C difficulties can be managed with a mix of process discipline and the right technology support. The complexity of the GSTR-9/9C changes for FY 2024-25 fundamentally demands a move from reactive year-end compliance to a model of continuous, automated reconciliation. The question is not if to automate, but how to integrate tax compliance seamlessly with core financial processes.

By adopting a comprehensive platform that incorporates AI-powered reconciliation, two-way vendor communication for issue resolution, and a continuous compliance framework, finance leaders can transform the annual return process. This shift ensures the GSTR-9/9C filing is a confirmation of compliance and an accurate financial closure, not a source of unexpected risk and financial drain.

Clear Finance Cloud is the dedicated tax module that integrates with your ERP to deliver these outcomes. Our platform provides the granular control, AI-powered accuracy, and automated workflows required for assured compliance and maximised working capital, turning complex annual filings into a strategic financial advantage.

By understanding where GSTR‑9 & GSTR‑9C difficulties usually arise and investing early in reconciliations, documentation and technology, businesses can convert year‑end GST filing from a fire‑fighting exercise into a predictable, well‑governed process.