Section 139(1) of the Income Tax Act

Income-tax Act, 2025: s.263

Section 139(1) falls under section 139 of the Income-tax Act, 1961, which corresponds to section 263 (Return of income) of the Income-tax Act, 2025.

Read section 263 of the 2025 Act

Correspondence checked against the ICAI tabular mapping of the two Acts and the BharatTax.co section commentary.

The decision most relied on for Section 139(1) is CIT v. Manjunatha Cotton & Ginning Factory (359 ITR 565), cited in 2,590 of the 8,117 judgments on BharatTax that turn on this section.

Leading authorities on Section 139(1)

CIT v. Manjunatha Cotton & Ginning Factory
359 ITR 565 · 2013 · High Court
2,590
citing judgments

A penalty notice issued under section 274 read with section 271(1)(c) is invalid if it fails to specify whether the penalty proceedings are initiated for concealment of income or for furnishing inaccurate particulars of income. This non-specification vitiates the penalty proceedings.

CIT v. AIMIL Ltd.
321 ITR 508 · 2010 · High Court
1,629
citing judgments

Employee contributions to PF and ESIC, deposited beyond the due date under the respective Acts but within the due date for filing the income tax return under Section 139(1), are allowable deductions under Section 36(1)(va). Such disallowance cannot be made during processing under Section 143(1).

Checkmate Services Pvt. Ltd. v. CIT
143 Taxmann.com 178 · 2022 · Supreme Court
1,392
citing judgments

Employee contributions to provident fund and ESI deposited by an employer beyond the due dates prescribed under the respective special Acts are not allowable as a deduction under section 36(1)(va) of the Income-tax Act, 1961. Such disallowance can be made during processing under section 143(1).

CIT v. Gujarat State Road Transport Corporation
366 ITR 170 · 2014 · High Court
1,158
citing judgments

Employees' contributions to welfare funds, such as provident fund, are not allowable as a deduction under section 36(1)(va) if deposited beyond the due date prescribed under the respective welfare statutes, even by a single day. Such delayed deposits are not cured even if made before the income-tax return filing due date.

CIT v. Pruthvi Brokers & Shareholders
349 ITR 336 · 2012 · High Court
956
citing judgments

Appellate authorities can entertain fresh claims or revised computations of income made by an assessee, even if these were not submitted through a revised return of income.

CIT v. SSA’s Emerald Meadows
73 Taxmann.com 241 · 2016 · High Court
791
citing judgments

A penalty notice under section 271(1)(c) read with section 274 of the Income Tax Act is invalid if it fails to specify whether the penalty is for concealment of income or for furnishing incorrect particulars of income.

Union of India v. Azadi Bachao Andolan
263 ITR 706 · 2003 · Supreme Court
691
citing judgments

A citizen is free to carry on business within the law, and mere tax planning without a motive to evade taxes through colorable devices is not frowned upon. The liability to taxation, for the purpose of tax treaty application, is a legal situation, not the fiscal fact of actual payment.

(i) CIT v. Merchem Ltd.
378 ITR 443 · 2015 · High Court
631
citing judgments

Belated remittance of employees' contribution to ESI and PF, even if deposited before the due date for filing the return of income under Section 139(1), is not allowed as a deduction. This disallowance falls under Section 36(1)(va) read with Section 2(24)(x), as Section 43B applies only to employer's contributions.

Co-operative Bank Ltd. v. CIT
384 ITR 490 · 2016 · High Court
631
citing judgments

Co-operative banks are not fundamentally different from co-operative societies, entitling them to claim deductions under Section 80P of the Income Tax Act, 1961, including for interest income treated as business income.

CIT v. Ghatge Patil Transports Ltd.
368 ITR 749 · 2014 · High Court
609
citing judgments

Deduction for employees' contributions to PF and ESIC is allowable under Section 43B if paid before the due date for filing the return under Section 139(1); similarly, delayed deposits of employers' contributions to ESIC and PF are also allowable.

Judgments on Section 139(1)

Mukut Behari Lal Bhargava, Gurgaon vs. ACIT, Circle(2)1, Gurgaon

In the result, the appeal of the assessee is partly allowed

ITA 2012/DEL/2025[2016-17]Status: DisposedITAT Delhi26 Nov 2025AY 2016-17

Bench: Shri Satbeer Singh Godara & Shri Manish Agarwalmukut Behari Lal Bhargava, Acit, Lcg 05, 04B Laburnum Complex, Circle-2(1), 1 4Th Floor, Sushant Lok 1, Vs. Gurgaon. Block-A, Sector-28 Haryana-122009. Pan-Adipb9356P (Appellant) (Respondent) Assessee By None Department By Shri Pradumna Kumar Singh, Sr. Dr Date Of Hearing 03.09.2025 Date Of Pronouncement 26.11.2025 O R D E R Per Manish Agarwal, Am: This Appeal Is Filed By The Assessee Against The Order Of The Ld. Commissioner Of Income Tax (Appeals), National Faceless Appeal Centre (Nfac), Delhi [Cit(A) In Short] In Appeal No. Cit(A), Gurugaon-1/10738/2018-19 Dated 05.02.2025 Passed U/S 250 Of The Income Tax Act, 1961 (The Act, In Short) For Assessment Year 2016-17. 2. Brief Facts Of The Case Are That The Assessee Is An Individual & Filed Its Return Of Income Declaring Total Income Of Rs.1,20,41,040/-. The Case Of The Assessee Was Selected For Limited Scrutiny & During The Course Of Assessment Proceedings, The Assessing Officer Has Issued Various Notices Which Were Replied By The Assessee. Mukut Behari Lal Bhargava Vs. Acit 3. Thereafter, The Assessment Order Was Passed At A Total Income Of Rs.1,79,36,182/- By Making Disallowance On Account Of Expenses Claimed On Costs Of Improvement Of Capital Asset, Disallowance Of Carry Forward Of Short Term Capital Gains & Long Term Capital Loss & Also Denied The Deduction Claimed U/S 80G Of The Act.

Section 250Section 271Section 80G

Satgramr. Colliery Employees Cooperative Credit Society Limited, Asansol vs. Assistant Commissioner of Income Tax, Circle-1, Asansol

In the result, the appeal of the assessee is allowed

ITA 1920/KOL/2025[2019-2020]Status: DisposedITAT Kolkata25 Nov 2025AY 2019-2020

Bench: Shri Sonjoy Sarma & Shri Rakesh Mishrai.T.A. No.1920/Kol/2025 Assessment Year: 2019-20 Satgram R Collery Employees Cooperative Credit Society Ltd……....Appellant Satgram Project, P.O Debichand Nagar, Block-Jamuria-1, Asansol, W.B. 713332. [Pan: Aajas8427K] Vs. Acit, Circle-1, Asansol……..……………....…..………………….…..... Respondent Appearances By: Shri Abhijit Banerjee, Advocate, Appeared On Behalf Of The Appellant. Shri S. B. Chakraborty, Addl. Cit, Sr. Dr, Appeared On Behalf Of The Respondent. Date Of Concluding The Hearing : November 24, 2025 Date Of Pronouncing The Order : November 25, 2025 आदेश / Order Per Sonjoy Sarma: This Appeal Filed By The Assessee Is Directed Against The Order Of The National Faceless Appeal Centre (Hereinafter Referred To As “Ld. Cit(A)”) Dated 03.02.2025 Passed Under Section 250 Of The Income-Tax Act, 1961 (Hereinafter Referred To As The “Act”). 2. At The Time Of Hearing Of The Matter, The Learned Representative Submitted That There Was A Delay Of 115 Days In Filing The Appeal. In This Connection, The Assessee Filed An Affidavit Explaining The Reasons For The Delay. After Considering The Submissions Of The Assessee & Examining The Contents Of The Affidavit, We Are Satisfied That The Reasons For The Delay Are Bona Fide & Deserve To Be Condoned.

Section 139(1)Section 143(1)Section 143(1)(a)Section 250Section 80P

St. Francis Xavier Church, Panvel vs. Income Tax Officer (Exemption), Thane

In the result, appeal of the assessee is allowed for statistical purposes

ITA 5883/MUM/2025[2024-25]Status: DisposedITAT Mumbai25 Nov 2025AY 2024-25

Bench: Justice (Retd.) Shri C.V. Bhadang & Shri Vikram Singh Yadavassessment Year : 2024-25 St. Francis Xavier Church Trust, Income Tax Officer, Plot 379/B, Behind Orion Mall Exemption Ward, Thane & S.T. Depot, Vs. Quershi Mansion, Panvel-410206. Gokhale Road, Pan : Aaets4913N Naupada, Thane-400602. (Appellant) (Respondent) For Assessee : None For Revenue : Smt. B. Brahma Vidya Date Of Hearing : 25-11-2025 Date Of Pronouncement : 25-11-2025 O R D E R Per Vikram Singh Yadav, A.M : This Is An Appeal Filed By The Assessee Against The Order Of The Learned Addl/Jcit(A)-Agra, Dated 29-07-2025, Pertaining To Assessment Year (Ay) 2024-25, Wherein The Assessee Has Taken The Following Grounds Of Appeal: “1.1. On The Facts & In Circumstances Of The Case & In Law The Learned Commissioner Of Income-Tax (Appeals) [Cit(A)] Erred In Confirming The Denial Of Exemption/Deductions Under Section 11 Of The Act Resorted To By The Centralized Processing Centre [Cpc), Income Tax Department, Bengaluru (The Learned Assessing Officer) While Processing The Return Of Income Under Section 143(1) Of The Act On The Grounds That The Audit Report In Form 10-Bb Was Filed Belatedly, Though With The Return Of Income Which Was Filed Within The Extended Time Limit Under Section 139(1) Of The Act.

For Appellant: NONEFor Respondent: Smt. B. Brahma Vidya
Section 11Section 11(1)(a)Section 11(2)Section 11(6)Section 12ASection 139(1)Section 143(1)Section 143(1)(a)