Quick Table of Contents
- What is GSTR-9?
- What is GSTR-9C?
- Who should file (and who usually doesn’t)
- Due date & late fee
- GSTR-9 vs GSTR-9C (difference table)
- Common mismatches that trigger scrutiny
- GST notices after annual filing (Section 61)
- What is DRC-03 and when to use it
- Sample professional reply line
- Best practices to avoid notices
- FAQs
What is GSTR-9?
GSTR-9 is the annual GST return that consolidates the information already reported in your periodic GST returns for the financial year.
It is meant to give the department a single-year snapshot of your outward supplies, inward supplies, ITC, and tax paid under GST.
What data is covered in GSTR-9?
- Outward supplies (sales) summary (B2B, B2C, exports, etc.).
- Inward supplies (purchases) summary, including reverse charge wherever applicable.
- Input Tax Credit (ITC) availed and reversed.
- Tax paid (CGST/SGST/IGST) and any differences.
- Amendments made in the year for earlier periods (as reflected in returns).
What is GSTR-9C?
GSTR-9C is a reconciliation statement that compares figures from your GST annual return with your financial statements/books to identify and explain differences.
From FY 2020-21 onwards, GSTR-9C is filed as a self-certified reconciliation statement (instead of CA/CMA certification), as per the changes notified in 2021.
What does GSTR-9C reconcile?
- Turnover as per books vs turnover as per GST returns.
- Tax paid vs tax payable based on reconciled turnover.
- ITC as per books vs ITC as per GST returns (and explanations for gaps).
Who should file (and who usually doesn’t)
GSTR-9 is filed by regular taxpayers, subject to exemptions/waivers notified from time to time (often linked to turnover thresholds).
GSTR-9C applies to taxpayers whose annual aggregate turnover exceeds ₹5 crore (as per current notified applicability).
- Regular taxpayers: Typically file GSTR-9 (if not exempted/waived).
- Turnover above ₹5 crore: File GSTR-9C in addition to the annual return.
- Special categories (like those with separate compliance frameworks): May not be required to file GSTR-9 depending on category and notifications.
Due date & late fee (GSTR-9)
The usual due date to file GSTR-9 is 31st December following the end of the financial year, unless extended by the government.
Late fee for GSTR-9 is ₹200 per day (₹100 CGST + ₹100 SGST/UTGST), capped at 0.25% of turnover in the State/UT per Act under each of CGST and SGST/UTGST (i.e., up to 0.5% total).
GSTR-9 vs GSTR-9C (difference table)
| Basis | GSTR-9 | GSTR-9C |
|---|---|---|
| Nature | Annual return (yearly consolidated return). | Reconciliation statement (books vs GST). |
| Applicability | Regular taxpayers, subject to exemptions/waivers. | Annual aggregate turnover > ₹5 crore. |
| Purpose | Summarizes the year’s GST reporting in one form. | Explains differences and ensures your books align with GST reporting. |
| Revision | No revision is allowed once filed. | No revision is allowed once filed. |
| Certification | Filed by taxpayer/authorized signatory. | Self-certified (CA/CMA certification removed from FY 2020-21 onwards). |
Common GSTR-9 / GSTR-9C mismatches (that create trouble)
Most GST problems after annual filing come from “data not matching” across GSTR-1, GSTR-3B, GSTR-2B, and your books—especially when the system flags differences during scrutiny.
Typical mismatch situations
- GSTR-1 sales ≠ GSTR-3B sales (timing, amendments, or reporting errors).
- ITC claimed in 3B > eligible ITC as per GSTR-2B (vendor non-filing, wrong GSTIN, timing issues).
- Turnover as per books > turnover shown in annual return (unbilled revenue, wrong classification, missed invoices).
- Credit note/debit note mismatch between returns and accounting.
- Wrong tax rate/HSN classification leading to short payment exposure.
After filing, discrepancies may be picked up under scrutiny of returns (Section 61), where the officer can issue a notice in Form GST ASMT-10 and seek an explanation.
Rule 99/Section 61 scrutiny generally provides up to 30 days to respond (or an extended time if permitted), and the reply is filed in Form ASMT-11.
Why these notices are commonly issued
- System-based comparison of returns vs books / annual return reconciliation.
- ITC mismatch (commonly linked to GSTR-2B vs 3B patterns) and eligibility concerns.
- Short payment indicators based on variance analysis.
How to reply without panic (practical steps)
- Identify the exact table/figure causing the mismatch (sales/ITC/tax rate/RCM).
- Prepare a clean reconciliation working: books → GST returns → annual return.
- If tax/interest is actually payable, consider paying voluntarily to reduce escalation risk.
- Attach supporting documents (trial balance, invoice lists, vendor communication, workings).
- Reply within the allowed time limit and keep the explanation crisp.
What is DRC-03 (and when should it be used)?
Form GST DRC-03 is used to make voluntary payment of tax, interest, and penalty based on self-ascertainment or when a liability is identified during proceedings.
It is commonly used when reconciliation reveals a genuine short payment and the taxpayer wants to settle it early to avoid longer demand/recovery proceedings.
Sample professional reply line
“The difference is due to timing and accounting classification. Detailed reconciliation with supporting documents is enclosed for kind perusal.”
Best practices to avoid GST notices (simple monthly routine)
- Reconcile GSTR-1 vs GSTR-3B every month before filing/closing books.
- Claim ITC carefully and track vendor filing so 2B doesn’t surprise you later.
- Do an annual reconciliation draft before filing GSTR-9 / GSTR-9C so the final filing is clean.
- Maintain invoice-level backups for large adjustments, credit notes, and reversals.
- File on time to avoid late fee exposure in annual return.
1) Can GST issue a notice even after filing GSTR-9C?
Yes—scrutiny can still happen if discrepancies are found during verification of returns and available information.
2) What if turnover in books is higher than turnover in GSTR-9?
It can be treated as a short payment risk unless the difference is properly explained and backed by reconciliation.
3) What if ITC claimed is higher than what seems eligible?
If reconciliation shows excess claim, voluntary payment/reversal with applicable interest may be required depending on facts, and DRC-03 is one route used for voluntary payments.
4) Can GSTR-9 be revised after filing?
No—GST law does not allow revision of GSTR-9 once filed.
5) Can GSTR-9C be revised after filing?
No—there is no provision to revise GSTR-9C once filed.
6) How much time is usually given to reply to a scrutiny notice?
Under Section 61/Rule 99 scrutiny workflow, the time to respond is generally up to 30 days (or extended time if permitted).
7) What documents should be attached with a notice reply?
- Reconciliation working (books vs returns).
- GSTR-1, GSTR-3B, and relevant period summaries.
- Trial balance / P&L / turnover working.
- Payment proof (DRC-03 challan) if paid voluntarily.
Disclaimer
This article is for informational purposes only and does not constitute legal, tax, or professional advice. GST laws and applicability conditions can change through notifications and amendments; consult a qualified tax professional for advice on your specific case.
