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First identify whether the Department has proposed an adjustment, flagged a defective return, issued an intimation or demand, or passed an adverse order. Those are different stages and may require different responses. Read the communication for the exact action requested, deadline, issuing authority, tax year and portal route; then respond or challenge the decision using the remedy that matches it.
Identify what the Department sent
“Rejected claim” can describe several different events. A proposed adjustment is not the same as a final assessment order, and an intimation or demand may call for a different response from a defective-return notice. Start with the notice or order itself rather than choosing a remedy based only on the claim that was denied.
Check the notice PDF and record:
- the issuing authority and the communication type;
- the assessment year or tax year and the statutory provision cited;
- the reason given for disallowing or adjusting the claim;
- what action the communication asks you to take and the response deadline;
- any proceeding limitation date and the portal route provided.
The Department’s e-Proceedings service handles, among other items, defective-return notices under section 139(9), proposed adjustments under section 143(1)(a), CPC intimations and demands, rectification communications, notices from tax authorities and “Seek for Clarification” requests. The user manual gives the portal path as Dashboard → Pending Actions → e-Proceedings. Income Tax Department: e-Proceedings; e-Proceedings User Manual.
Choose a route that matches the communication
| What you received | What to consider | Deadline or key limit |
|---|---|---|
| Defective-return notice under section 139(9) | Correct the defect as directed in the notice, or use an available extension or adjournment option if needed. | The Department says generally 15 days from receipt or the period specified in the notice. Check the notice’s own deadline and directions. Income Tax Department: e-Proceedings. |
| Proposed adjustment under section 143(1)(a) | Respond by agreeing with the discrepancy or disagreeing and explaining why. A revised return under section 139(5) may be possible where applicable; eligibility and deadline depend on the year and circumstances. | The Department’s user manual says to respond within 30 days from issue of the notice. Income Tax Department: proposed adjustment guidance. |
| Processed-return intimation, reduced refund or demand | Consider online rectification if the issue is a mistake apparent from the record; see the rectification section below. | Check the relevant portal option and the decision or communication for its instructions. Income Tax Department: rectification guidance. |
| Adverse assessment or other appealable order | Consider a first appeal if you dispute the order’s legal or factual conclusion rather than seeking correction of an apparent record error. | Relevant first appeals generally have a 30-day period, but the trigger and applicable form depend on the governing Act and order type. Income Tax Department: appeals guidance; Form 99 User Manual. |
| Rectification request rejected or CPC correction unavailable | Check whether the Department’s specified route to the Jurisdictional Assessing Officer applies, or whether an appealable rectification order has been issued. | These are distinct procedural situations; follow the decision and portal options for the case. Income Tax Department: rectification guidance. |
Reply to a notice or proposed adjustment
When a communication invites an electronic response, use the route in the notice and the e-Proceedings account. The Department describes e-Proceedings as an electronic platform for conducting proceedings end to end on the e-Filing portal; a registered user or authorised representative can view and respond to notices, intimations and letters. Income Tax Department: e-Proceedings.
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For a proposed adjustment, address the specific discrepancy in the notice. If you disagree, explain why the claim should not be adjusted and provide records that support that explanation. If you agree, respond accordingly and consider whether any permitted correction, such as a revised return where eligible, is available. Do not assume that option is open for every year or after every deadline.
Before submitting, check that the response addresses the point raised and that the attachments are legible and relevant. The Department says a submitted e-Proceedings response cannot be edited, updated or withdrawn. Save the acknowledgement and a copy of the response and documents for your records. Income Tax Department: e-Proceedings.
Use rectification only for an apparent record mistake
Rectification is intended for a mistake apparent from the record in a covered CPC intimation or order. It is not a general way to introduce a new deduction or exemption that was not part of the record. If CPC processed the return and the result is a demand or reduced refund, the Department says a taxpayer can request online rectification through the e-Filing account. In specified circumstances, its FAQ describes submitting a request to the Jurisdictional Assessing Officer when the portal does not allow the relevant CPC correction. Income Tax Department: rectification guidance.
If a rectification request is rejected, check the exact decision and remedy stated. The Department describes escalation to the Jurisdictional Assessing Officer in specified cases and separately confirms that an appeal may be filed directly against a CPC rectification order. A portal submission problem or rejected request is not automatically the same as an appealable order.
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Consider an appeal when you dispute an adverse order
An appeal may be appropriate when the dispute concerns the legal or factual conclusion in an adverse order, rather than a mistake that is apparent from the existing record. The Department describes first appeals to the Joint Commissioner (Appeals) or Commissioner of Income Tax (Appeals), depending on the order and applicable law. Income Tax Department: appeals guidance.
For an order under the Income Tax Act, 1961, the Department’s Form 35 guidance gives a 30-day period from service of the order or demand, as applicable, and says delay may be condoned for reasonable cause. For the 2025 Act process, the Form 99 manual states a 30-day limit tied to service of the notice of demand for an assessment or penalty appeal, or service of the appealed order in other cases. These are general official instructions: calculate your deadline using the actual order, service date, applicable form and governing Act. Income Tax Department: appeals guidance; Form 99 User Manual.
Set out the order being challenged, the grounds for disagreement and the relevant facts. Connect each ground to records that support the particular claim and address the reason the Department gave for disallowing it. The necessary evidence depends on the claim and the issue in the order; there is no single checklist that fits every appeal.
Independent reader supportYour contribution helps us test, update, and keep practical guides available for everyone.Check which Income Tax Act applies
The Income Tax Act, 2025 took effect on 1 April 2026. The Department says proceedings relating to tax years beginning before that date—including proceedings initiated on or after it—continue under the Income Tax Act, 1961. Its return FAQ says AY 2026–27 and earlier matters continue under the old Act, while Tax Year 2026–27 is a separate compliance year under the new Act. Identify the relevant assessment year or tax year before relying on a section number or form; the date a notice arrived does not by itself determine the governing Act. Income Tax Department: transition to the Income Tax Act, 2025.
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Do not wait for the portal to close
The portal’s response window may close before the proceeding limitation date. The Department FAQ says that, while proceedings remain open, submission is ordinarily available only until seven days before the proceeding limitation date, up to 6 p.m.; the authority may re-enable submission in some cases. It also says the portal can disable a CPC response after its due date. Use the date displayed in your account and the notice, and act early enough to resolve access or document problems. Income Tax Department: e-Proceedings.
When professional help is useful
Consider consulting a qualified Indian chartered accountant or tax professional when an adverse order involves a significant amount, the facts or law are disputed, multiple proceedings overlap, or an appeal deadline is close. A professional can help identify the governing Act, the correct remedy and the grounds and records relevant to your case.
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