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Reply to Notice Under Section 139(9) — Defective Return Draft

Complete guide to reply under Income Tax Act. Computation, examples, old vs new regime, latest Finance Act changes. Updated March 2026.

Published
Updated
Reading time
8 min
Questions
4 answered
  • High Complexity
  • In-Depth Guide
Topic
Income Tax
Published
March 23, 2026
Last updated
Mar 23, 2026
Reading time
8 min
0:00
Last updated: March 2026Verified against: Government sources

Overview

This article provides a detailed, plain-language explanation of Reply to Notice Under Section 139(9) under the Income Tax Act, 1961, Income Tax Rules, 1962, and the new Income Tax Act, 2025 (where applicable). This guide incorporates all amendments made by the Finance Act, 2025, Finance Act, 2024 (July Budget), and relevant CBDT Circulars and Notifications up to March 2026.

Relevant provisions: Section 139(9). Where the Income Tax Act, 2025 makes changes, a comparison with the existing law is provided.

Why This Matters
Non-compliance with income tax provisions related to reply can result in interest under Sections 234A/234B/234C (up to 1% per month), penalty under Section 270A (50% to 200% of tax on under-reported income), prosecution under Sections 276C-277 (imprisonment up to 7 years for tax evasion), and disallowance of deductions or exemptions. Understanding these provisions helps you stay compliant, minimize tax legally, and avoid disputes with the Income Tax Department.

What the Law Says

Provisions Under Income Tax Act, 1961

Section 139(9) of the Income Tax Act, 1961 governs reply. The section establishes: (a) the scope of taxability, (b) computation methodology, (c) deductions and exemptions available, (d) compliance requirements, and (e) consequences of non-compliance. The Income Tax Rules, 1962 provide detailed procedural requirements including prescribed forms, methods of valuation, and timelines.

Changes Under Income Tax Act, 2025

New Income Tax Act 2025
The Income Tax Act, 2025 (passed in the Budget Session) is set to replace the 1961 Act. Key changes relevant to reply include:

1. Tax Year Concept: The Previous Year/Assessment Year system is being replaced with a unified "Tax Year" concept, simplifying compliance.

2. Simplified Language: The new Act uses clearer, more modern language with fewer cross-references and provisos.

3. Rationalized Provisions: Many overlapping sections have been merged, redundant provisions removed, and the overall structure streamlined from 298 sections to about 536 clauses organized in 23 chapters.

4. Default New Regime: The new tax regime (lower rates, fewer deductions) continues as the default under the new Act.

5. Transition: The new Act will apply from a date to be notified. Until then, the Income Tax Act, 1961 remains fully operative. All references in this article to specific sections are to the 1961 Act unless stated otherwise.

Who Is Affected?

Taxpayer CategoryApplicable?Special Provisions
Salaried IndividualYesStandard deduction Rs. 75,000 (new regime) / Rs. 50,000 (old regime); Form 16 from employer
Self-Employed / ProfessionalYesPresumptive taxation u/s 44ADA if gross receipts up to Rs. 75 lakh (with digital receipts)
Business Owner / ProprietorYesPresumptive u/s 44AD if turnover up to Rs. 3 crore (with digital receipts); otherwise regular books
Company (Domestic)Yes22% tax u/s 115BAA or 25%/30% normal rate; MAT u/s 115JB at 15%
LLP / Partnership FirmYes30% flat rate + surcharge if income above Rs. 1 crore
HUFYesSame slab rates as individual; separate entity for tax
Trust / SocietyYesExempt if registered u/s 12A/12AB; otherwise taxable at MMR/slab
NRI / Foreign CompanyYesOnly Indian-sourced income taxable; DTAA benefits available; special rates u/s 115A
Investor (Equity/MF/Crypto)YesSTCG 20% (equity), LTCG 12.5% (equity) above Rs. 1.25 lakh; VDA 30% flat
Senior Citizen (60+/80+)YesHigher basic exemption (old regime); no advance tax if no business income u/s 207; higher 80D limits

Detailed Explanation with Practical Examples

Example 1 (Salaried): Rahul works in an IT company in Faridabad earning Rs. 12 lakh per annum. Under the new tax regime (default from FY 2024-25), his tax computation is:

ParticularAmount (Rs.)
Gross Salary12,00,000
Less: Standard Deduction(75,000)
Taxable Income11,25,000
Tax (New Regime Slab FY 2025-26)
0-4,00,000: Nil0
4,00,001-8,00,000: 5%20,000
8,00,001-12,00,000: 10%32,500
Total Tax52,500
Less: Rebate u/s 87A (if income up to Rs. 12 lakh)(52,500)
Tax PayableNIL
Health & Education Cess 4%0
Net Tax PayableNIL

Example 2 (Business): Priya runs a trading business with turnover of Rs. 1.5 crore (90% digital receipts). She can opt for presumptive taxation u/s 44AD and declare 6% of digital turnover as income = Rs. 9 lakh. Since this is below the basic exemption + deductions, her tax liability could be minimal.

Example 3 (Capital Gains Post-July 2024): An investor sells listed equity shares held for 18 months at a profit of Rs. 3 lakh. Post-Finance Act 2024 changes: LTCG on listed equity is taxed at 12.5% (reduced from earlier 10%) with exemption of Rs. 1.25 lakh. Tax = 12.5% of (3,00,000 - 1,25,000) = Rs. 21,875 + 4% cess = Rs. 22,750.

Tax Planning Advice
For reply, compare your liability under both old and new tax regimes before choosing. The new regime offers lower rates but fewer deductions. If you have significant deductions (home loan, 80C, 80D, HRA), the old regime may still save more tax. Use a tax calculator or consult a CA. our tax experts help you choose the optimal regime --
Quick recapKey facts & short answers

Key Facts About Reply to Notice Under

  • Applies in: All states across India, under the relevant central law.
  • Mode: Mostly online via the official government portal.
  • Typical timeline: Ranges from a few days to a few weeks depending on the case.
  • Non-compliance: May attract penalties, interest or late fees.
  • Expert help: TaxClue completes Reply to Notice Under end to end for you.

What is reply?

Section 139(9) of the Income Tax Act governs reply. It covers computation, exemptions, deductions, and compliance requirements.

What changes under new Income Tax Act 2025?

The new Act simplifies language, replaces PY/AY with Tax Year, and rationalizes provisions. Substantive changes are limited. Effective date to be notified.

A due date missed is rarely a matter of law — it is almost always a matter of calendar.

— TaxClue Compliance Desk

Reply to Notice Under: a key compliance topic in Indian tax and corporate law that businesses and individuals must understand to remain compliant.

READY DRAFTReply to Notice u/s 139(9) — Defective Return

A response to a notice under section 139(9) treating your return as defective, either rectifying the defect by filing a corrected return or explaining why the return is not defective.

INCOME-TAX DEPARTMENT — CENTRALISED PROCESSING CENTRE (CPC), BENGALURU
Response filed through the e-Filing portal under the
"Defective Return u/s 139(9)" service.

Name of Assessee   : [Name of Assessee]
PAN                : [ABCDE1234F]
Assessment Year    : [A.Y. 20__-__]
Original Ack. No.  : [Acknowledgement number] dated [DD/MM/YYYY]
Communication Ref. : [CPC communication / DIN] dated [DD/MM/YYYY]
Error Code(s)      : [e.g. 14 / 31 / 38 / 86 / 202]
Response Date      : [DD/MM/YYYY]

To,
The Assistant Commissioner of Income-tax (CPC),
Centralised Processing Centre, Bengaluru.

Subject: Response to notice under section 139(9) of the Income-tax Act,
         1961 — return treated as defective for A.Y. [20__-__] — reg.

Respected Sir/Madam,

1.  This is with reference to the intimation under section 139(9) dated
    [DD/MM/YYYY] communicated by CPC, whereby the return of income filed by
    the assessee for A.Y. [20__-__] vide acknowledgement no. [___] has been
    treated as defective for the following reason (Error Code [__]):

    "[Reproduce the exact defect described in the notice, e.g. 'Gross
    receipts shown in Form 26AS/TDS are not offered as income' / 'Books of
    account not maintained / Balance Sheet and P&L not filled although
    income under head PGBP is declared' / 'Tax has not been paid on the
    returned income']."

2.  The assessee submits as under:

    [OPTION A — where the defect is accepted and rectified]
    The defect is duly rectified by filing a corrected return in the
    prescribed ITR form. In the corrected return: [state correction, e.g.
    "the receipts of ₹[amount] appearing in Form 26AS have been offered
    under the head [___]" / "the Balance Sheet and Profit & Loss items in
    the 'No account case' schedule have been completed" / "the self-
    assessment tax of ₹[amount] has been paid vide challan CIN [___] dated
    [DD/MM/YYYY] and incorporated"]. The corrected return has been
    uploaded/e-verified on [DD/MM/YYYY].

    [OPTION B — where the return is not defective]
    With respect, the return is not defective because [explanation, e.g.
    "the receipts flagged pertain to [exempt/already-offered] income and
    are duly reflected in Schedule [__]" / "the assessee is covered by the
    presumptive scheme under section 44AD/44ADA and is not required to
    maintain regular books, hence the P&L/Balance Sheet schedules are not
    applicable"]. It is therefore requested that the original return filed
    on [DD/MM/YYYY] be accepted as valid.

3.  A reconciliation of income offered vis-à-vis Form 26AS / AIS / TIS is
    enclosed at Annexure-[__], demonstrating that all receipts stand duly
    accounted for.

PRAYER
It is prayed that the [corrected return filed in response be treated as a
valid return relating back to the date of the original return] / [original
return be accepted as valid, the defect notice being not applicable to the
assessee's case], and the return be processed under section 143(1)
accordingly.

List of enclosures:
  1. Copy of section 139(9) intimation.
  2. Copy of original / corrected return and computation.
  3. Reconciliation with Form 26AS / AIS.
  4. Challan for self-assessment tax, if paid.

Thanking you,

Yours faithfully,

For [Name of Assessee]

______________________________
[Signature — Assessee / Authorised Representative]
Name : [Name]     PAN: [ABCDE1234F]
Place: [City]     Date: [DD/MM/YYYY]
▸ How to use & important notes
  • Respond within 15 days of the notice (extension can be sought online); if you do not respond, the return is treated as invalid — i.e. as if no return was filed.
  • Rectify the defect through the portal by choosing "Agree" and uploading the corrected return, or "Disagree" with a clear reason — do not merely e-mail a letter.
  • Common error codes: unpaid self-assessment tax, P&L/Balance Sheet not filled, 26AS receipts not offered, and wrong ITR form; fix the actual cause, not just the symptom.
  • A validly rectified return relates back to the original filing date, preserving your original due-date benefits.

Disclaimer: This is a general-purpose template for reference only. Facts, figures, stamp duty and clauses vary with your situation and state law — have it reviewed before use. Need this professionally drafted, stamped and filed? Talk to a TaxClue expert.

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Disclaimer: This article is for general informational purposes only and does not constitute professional tax, legal or financial advice. Laws, rates and due dates change and can vary by individual case — always verify with the relevant government source (e.g. mca.gov.in, incometax.gov.in) or consult a qualified professional before acting. TaxClue accepts no liability for decisions taken based on this content.

People also ask

Questions, answered

Short, direct answers to the 4 questions readers ask most on this topic.

Section 139(9) of the Income Tax Act governs reply. It covers computation, exemptions, deductions, and compliance requirements.

The new Act simplifies language, replaces PY/AY with Tax Year, and rationalizes provisions. Substantive changes are limited. Effective date to be notified.

Late fee u/s 234F (Rs. 5,000), interest u/s 234A/B/C (1% per month), penalty u/s 270A (50-200% of tax), prosecution for tax evasion above Rs. 25 lakh.

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