How to Respond to an Income Tax Notice Through e-Proceedings on the e-Filing Portal

Opening the e-Filing dashboard to find a red "Pending Actions" badge is the moment most salaried taxpayers panic. Yet under the faceless regime that has governed Indian assessments since the Taxation and Other Laws Act took effect on 13 August 2020, almost every routine query is now resolved entirely online through the e-Proceedings facility, with no visit to any income-tax office. This guide walks through exactly what to do when a notice lands, using the official e-Proceedings user manual published on incometax.gov.in as the reference and a worked salary example under the FY 2025-26 (AY 2026-27) new regime.

The Scenario

You are a salaried employee who filed the return for AY 2026-27 in July 2025 and expected a refund of Rs 8,000. Instead, on 20 October 2025 the portal shows a Pending Action flagged as a "Prima Facie Adjustment" communication. On logging in you find the Centralised Processing Centre (CPC) at Bengaluru proposes to add back Rs 50,000 you had claimed as an NPS deduction under Section 80CCD(1B), because that deduction is not admissible under the new regime you had opted into. The system gives you 30 days to agree or disagree before the adjustment is finalised.

This single scenario touches the three notice types that account for the overwhelming majority of e-Proceedings traffic: a Defective Return notice under Section 139(9), an intimation and adjustment proposal under Section 143(1)(a), and a rectification under Section 154. The mechanics of responding are identical across all of them, so mastering one prepares you for all. If you have not yet mapped your own tax position, run the numbers first on the income tax calculator so you know what the correct figure should be before you agree or disagree with the department.

Statutory Answer

The legal spine of the whole process is Section 143(1) of the Income-tax Act, 1961. Its proviso, inserted to enable pre-adjustment intimation, requires that before CPC makes any adjustment for an arithmetical error, an incorrect claim apparent from the return, or a disallowance apparent from the audit report, it must give the taxpayer an opportunity to respond. Clause (a) of Section 143(1) lists the six categories of permissible adjustment, and the second proviso mandates that a response window of 30 days be given; if no response is filed within that period, the adjustment is made and reflected in the final intimation. You can read the section text on the official statute repository at indiacode.nic.in.

A Defective Return notice under Section 139(9) is different in consequence. When a return is treated as defective (for example, tax was paid but income details are incomplete, or the balance sheet is missing where required), the Assessing Officer gives you 15 days to remedy the defect. If you do not respond within 15 days (or such extended period the officer allows on your written request), the return is treated as invalid, meaning in law you are deemed never to have filed it, with all the interest and penalty consequences of a missed ITR filing. A Section 154 rectification covers "any mistake apparent from the record" and can be initiated either by you or suo-moto by the authority; the department must dispose of a taxpayer's rectification application within six months from the end of the month in which it is received.

Two anchoring facts to keep in mind. First, responding on the portal requires an Active PAN (an Active TAN for TDS/TAN-side proceedings), per the incometax.gov.in e-Proceedings manual. Second, a successful submission always returns a Transaction ID on screen, which is your only proof of compliance, so record it. For the tax deducted that seeded this whole mismatch, the concepts are set out in our glossary entries on TDS and Form 16.

Worked Resolution

Take Meera, a salaried employee with a gross salary of Rs 14,00,000 for FY 2025-26 who opted into the new regime. Under the new regime the standard deduction is Rs 75,000 (against Rs 50,000 in the old regime), so her taxable income should have been Rs 13,25,000. But she also claimed Rs 50,000 under Section 80CCD(1B), and Section 80CCD(1B) is not allowed in the new regime (it is available only in the old regime), dropping her declared taxable income to Rs 12,75,000. CPC's Section 143(1)(a) proposal simply restores the Rs 50,000.

The FY 2025-26 new-regime slabs are set out below, and you can pressure-test any figure against the new regime calculator.

Now compare the tax Meera declared with the tax CPC computes after the adjustment. Because both figures exceed the Rs 12,00,000 threshold, the enhanced Section 87A rebate of Rs 60,000 in the new regime does not apply to either.

The additional demand is Rs 81,900 minus Rs 74,100 = Rs 7,800, and the earlier expected tax refund of Rs 8,000 shrinks accordingly. Meera's correct move is to open the communication, read the proposed adjustment, and click Agree with the disallowance, since 80CCD(1B) genuinely cannot be claimed in the new regime. Had CPC instead been wrong (say it had ignored a valid Section 80C claim she made under the old regime), she would click Disagree, attach the supporting proof, and cite the exact reason. Before choosing, taxpayers unsure which regime serves them should compare both on the old vs new regime calculator.

The step-by-step submission

The path in the portal, per the official manual, is precise. Log in at incometax.gov.in, go to Dashboard > Pending Actions > e-Proceedings, and choose the Self tab (or the relevant PAN/TAN). Select the specific proceeding, view or download the notice PDF, then click Submit Response. For a 143(1)(a) adjustment you mark each proposed item as Agree or Disagree; for a Defective Return under 139(9) you either file a corrected/revised return or explain why the return is not defective. Attach documents where you disagree, submit, and save the Transaction ID. The entire loop, from notice to closure, is faceless and paperless as designed under the 2020 faceless-assessment framework.

FAQ

How many days do I get to respond to a Section 143(1)(a) adjustment?

You get 30 days from the date of the intimation to agree or disagree, under the second proviso to Section 143(1). If you file no response within 30 days, CPC proceeds to make the proposed adjustment and issues the final intimation reflecting the revised tax, as stated in the incometax.gov.in e-Proceedings manual.

What happens if I ignore a Defective Return notice under Section 139(9)?

If you do not rectify the defect within the 15 days allowed (or an extended period the Assessing Officer grants on your written request), the return is treated as invalid under Section 139(9). In law you are then deemed never to have filed, exposing you to interest under Sections 234A/234B/234C and possible penalty for the relevant assessment year.

Can I revise my response after I have submitted it?

Once you submit and receive a Transaction ID, that response is recorded against the proceeding. You cannot casually overwrite it, so verify every figure before clicking submit. If you later discover a genuine mistake apparent from the record, the correct route is a separate Section 154 rectification, which the department must dispose of within six months from the end of the month it is received.

Do I need a Digital Signature Certificate to respond?

For most individual salaried taxpayers, an Electronic Verification Code (EVC) through Aadhaar OTP, net banking, or a pre-validated bank account is sufficient to authenticate the submission. A Digital Signature Certificate (DSC) is mandatory only where the law otherwise requires the return itself to be signed with a DSC, such as for entities subject to audit, per the incometax.gov.in verification rules.

The notice says my TDS does not match Form 26AS. What do I do?

This is one of the six adjustment grounds under Section 143(1)(a). Compare your claimed credit against Form 26AS and the Annual Information Statement (AIS) on the portal. If your employer deducted but mis-reported the TDS, ask them to file a correction statement; if your own claim was overstated, click Agree. Our TDS glossary entry explains how the credit chain is meant to reconcile.

Is there a fee to respond to a notice through e-Proceedings?

No. Responding to any notice or communication through e-Proceedings on incometax.gov.in carries no government fee. A fee arises only if you escalate to a formal appeal in Form 35 before the Commissioner (Appeals), which is a separate remedy from replying to a routine CPC adjustment.

What if I genuinely need more time than the deadline allows?

For a Defective Return under Section 139(9), you can file a written request to the Assessing Officer seeking extension beyond the initial 15 days, and the officer may condone the delay. For a 143(1)(a) adjustment, the 30-day window is firm, so if you are missing a document, it is safer to submit a partial Disagree with the reason recorded rather than let the window lapse and have the adjustment made automatically.