Section 139(9) Defective Return Notice: Complete Guide to Fixing Your ITR:

Received a Section 139(9) notice after filing your ITR? Understand why it was issued, how to fix the defect, and how to avoid your return being treated as invalid.

Here's How to Fix It Before It's Too Late

Khush Trivedi

Jul 8, 2026

Last update on Jul 8, 2026

Filled your ITR? & got the notice us 139(9)? & don’t know what it is & why its been issued?

Let’s decode it

“Where the Assessing Officer considers that the return of income furnished by the assessee is defective, he may intimate the defect to the assessee and give him an opportunity to rectify the defect within a period of fifteen days from the date of such intimation or within such further period which, on an application made in this behalf, the Assessing Officer may, in his discretion, allow; and if the defect is not rectified within the said period of fifteen days or, as the case may be, the further period so allowed, then, notwithstanding anything contained in any other provision of this Act, the return shall be treated as an invalid return and the provisions of this Act shall apply as if the assessee had failed to furnish the return.

If no response is given return will be discarded as if it was never filled.

Common Defect Scenarios & Fixes

Defect category	Typical trigger	Practitioner fix
TDS/TCS credit claimed, income not reported	Interest, salary, rent, professional receipts with TDS shown in 26AS/AIS but income not offered to tax	Report the corresponding income under the correct head of which TDS has been deducted
Gross receipts/turnover in 26AS/AIS exceed ITR	26AS/AIS/TIS shows higher receipts than declared under any head	Reconcile head-wise explain genuine exclusions (GST, reimbursements) in the response if disagreeing
Wrong ITR form used	Capital gains/foreign assets/business income reported in ITR-1 or ITR-4 where ITR-2/3 was mandatory	Re-file in the correct form carry all schedules forward accurately
P&L / Balance Sheet not filled	Business/profession income (ITR-3) filed without Schedule BS/P&L, or incomplete	Complete both schedules; ensure no-books-of-account option used only where genuinely eligible
Audit report missing/incomplete	Turnover exceeds Sec 44AB threshold but tax audit report not linked/uploaded before filing	Upload/link Form 3CA-3CD or 3CB-3CD; confirm UDIN and filing date
Presumptive income inconsistencies	44AD/44ADA/44AE gross receipts don't match 26AS, or profit % below prescribed rate without maintaining books	Correct gross receipts figure; if books not maintained, ensure declared profit meets the minimum %
Tax payment shortfall/challan mismatch	Self-assessment tax shown as paid but challan BSR code/serial not reflected, or tax due but unpaid before filing	Pay balance tax with interest u/s 234A/B/C first, then quote correct challan details in the revised return
Return not verified within time	ITR filed but e-verification/ITR-V not completed, sometimes flagged along with other defects	Complete e-verification

How to submit Response

1. Login to the e-filing portal → Pending Actions → e-Proceedings → download the notice PDF (password: PAN in lower case + DOB as DDMMYYYY).

Route	Use when	Action
Agree	The flagged defect is genuine a real omission, wrong form, or mismatch	File the corrected return online (offline utility/JSON) under the same notice reference before the deadline
Disagree	The AIS/26AS entry is not the assessee's, is duplicated, or the original return was in fact correct	Submit a reasoned explanation with supporting evidence (bank certificate, TDS reconciliation, AIS feedback filed) do not leave the box blank