Filing your Income Tax Return (ITR) does not always mean that the process ends there. After you file your return, the Income Tax Department processes the information reported in your ITR and compares it with details available in Form 26AS, Annual Information Statement (AIS), Taxpayer Information Summary (TIS), TDS statements, bank information, property transactions, securities transactions and other reported financial data.

If the department notices an error, mismatch, missing information or any issue requiring clarification, you may receive an income tax notice, intimation or communication. Receiving an income tax notice after filing your ITR does not automatically mean that you have committed tax evasion or that a penalty will be imposed. Some communications are routine and may simply require you to correct a mistake or provide additional information.

However, you should never ignore an income tax notice. In this article, we explain the most common income tax notices received after filing an ITR, what each notice means and how taxpayers should respond.

Important: For returns relating to Assessment Year 2026–27, proceedings continue under the Income-tax Act, 1961. Therefore, familiar section numbers such as 139(9), 143(1), 143(2) and 142(1) continue to be relevant for these returns.

Why Do You Receive an Income Tax Notice After Filing ITR?

The Income Tax Department receives financial information about taxpayers from several sources. Therefore, your ITR is not examined in isolation.

A notice or communication may be generated because of:

mismatch between ITR and Form 26AS;
mismatch between ITR and AIS/TIS;
TDS claimed without reporting corresponding income;
incorrect selection of ITR form;
omission of salary, interest, capital gains or business income;
incorrect deduction or exemption claim;
high-value financial transactions;
incorrect calculation of tax;
non-reporting of foreign income or foreign assets, where applicable;
difference between turnover reported in ITR and information available with the department;
carry-forward of an incorrect loss;
outstanding income tax demand from an earlier year; or
selection of the return for scrutiny.

Therefore, before responding, you should first understand which section the communication has been issued under and what exactly the department is asking for.

1. Defective Return Notice Under Section 139(9)

One of the most common notices taxpayers may receive after filing an ITR is a Defective Return Notice under Section 139(9). A return can be considered defective when required information is incomplete, inconsistent or incorrectly reported.

For example, the Income Tax Department specifically identifies situations such as claiming TDS credit without reporting the corresponding income or having business/professional income without properly completing the required Balance Sheet and Profit & Loss schedules.

Common Reasons for Section 139(9) Notice

You may receive a defective return notice because:

the wrong ITR form was used;
TDS has been claimed but related income has not been reported;
business income has been reported without completing the applicable financial statements;
gross receipts reported in the ITR do not match information appearing in Form 26AS;
required schedules are incomplete;
tax has been calculated but income has been incorrectly reported as nil;
mandatory information has not been entered; or
information reported in different schedules of the ITR is inconsistent.

Time Limit to Respond

Generally, the taxpayer gets 15 days from the date of receiving the notice or the period specifically mentioned in the notice to rectify the defect. An extension may also be requested through the portal where permitted.

What Happens If You Ignore Section 139(9)?

Ignoring a defective return notice can be serious. If the defect is not rectified within the permitted time, the return may be treated as invalid.

Consequently, the taxpayer may face issues such as:

return being treated as not properly filed;
loss of carry-forward of eligible losses;
interest consequences;
loss of certain exemptions or benefits; and
other consequences depending on the facts of the case.

How to Reply to Section 139(9)

Dashboard → Pending Actions → e-Proceedings → For Your Action

Download the notice, understand the defect and submit the corrected information. If you agree with the defect, correct the return accordingly.

If you believe that the return is correct, you can disagree and provide an appropriate explanation with supporting information. Once a response is submitted through the portal, it generally cannot be edited or withdrawn, so review it carefully before submission.

2. Intimation Under Section 143(1)

Many taxpayers become worried when they receive an email mentioning Section 143(1). However, Section 143(1) is generally an intimation after processing of the return, rather than a scrutiny notice by itself.

The Centralized Processing Centre (CPC) processes your ITR and compares the tax calculation and information reported in your return. The intimation may show:

No Demand – No Refund

Your return has been processed without any additional tax payable or refund.

Refund Payable

The department accepts that a refund is due to you.

Tax Demand Payable

The department’s computation differs from your return and additional tax may become payable. An intimation under Section 143(1) can generally be issued within nine months from the end of the financial year in which the return is filed.

What Should You Check in a 143(1) Intimation?

Compare the department’s computation with your filed ITR carefully.

Check:

total income;
deductions claimed;
TDS credit;
TCS credit;
advance tax;
self-assessment tax;
tax payable;
interest;
refund amount; and
adjustments made by CPC.

Do not simply pay a demand because an amount appears in the intimation. First determine why the difference has arisen. If there is a mistake apparent from the record in a processed return, the e-Filing portal also provides a rectification facility subject to the applicable conditions.

3. Proposed Adjustment Under Section 143(1)(a)

Before CPC makes certain adjustments while processing an ITR, the taxpayer may receive a communication proposing an adjustment under Section 143(1)(a).

This could happen where, for example:

information in one schedule is inconsistent with another;
an incorrect claim is apparent from the return;
certain income reflected in available information has not been appropriately considered; or
an adjustment is otherwise permissible during processing.

A taxpayer should not ignore this communication. Read the reason for the proposed adjustment, compare it with the ITR and supporting documents and either agree or disagree with proper justification. The Income Tax Department’s guidance provides for responding to prima facie adjustment communications through the e-Proceedings facility.

4. Scrutiny Notice Under Section 143(2)

A notice under Section 143(2) is more significant than a routine 143(1) intimation. It generally means that the Income Tax Department has selected your return for scrutiny assessment.

The purpose is to verify that:

income has not been understated;
excessive loss has not been claimed;
tax has not been underpaid; and
claims made in the return can be supported.

For returns governed by the Income-tax Act, 1961, a Section 143(2) notice is generally required to be served within three months from the end of the financial year in which the return was furnished.

Why Can an ITR Be Selected for Scrutiny?

Possible reasons may include:

unusually large deductions;
substantial capital gains or losses;
high-value property transactions;
significant share or derivatives transactions;
differences between reported income and available information;
foreign transactions;
significant cash transactions;
business turnover discrepancies;
specific information available with the tax department; or
risk-based selection through departmental systems.

However, receiving a scrutiny notice does not itself prove that the taxpayer has made an incorrect claim.

How Should You Respond?

First identify the exact issue raised. Then prepare supporting documents such as:

bank statements;
Form 16;
Form 16A;
Form 26AS;
AIS;
books of account;
invoices;
sale and purchase documents;
capital gain workings;
property purchase/sale deeds;
investment proofs;
deduction documents;
loan documents; and
other relevant evidence.

Respond point by point instead of uploading a large number of unrelated documents. A concise, factual and properly documented response is usually much stronger than an unnecessarily lengthy reply.

5. Notice Under Section 142(1)

A notice under Section 142(1) may be issued by the Assessing Officer for obtaining information required for assessment.

The Assessing Officer may ask the taxpayer to:

furnish a return where required;
provide accounts or documents;
explain particular transactions; or
furnish information relevant to the assessment.

Section 142 specifically gives the Assessing Officer power to call for information for the purpose of making an assessment.

Example

Suppose a taxpayer reports business income of ₹12 lakh, but the department has information showing substantial bank deposits during the year.

The Assessing Officer may ask for:

bank statements;
nature and source of deposits;
books of account;
sales details;
GST returns;
loan confirmations; and
supporting documents.

The taxpayer should provide a proper reconciliation explaining the transactions. Do not submit false explanations or fabricated documents merely to reconcile figures. The response should always be based on actual records.

6. Notice Regarding Adjustment of Refund Against Outstanding Demand – Section 245

Sometimes your current year’s ITR may result in a refund, but an old income tax demand is outstanding against your PAN. In such cases, the Income Tax Department may propose to adjust the refund against the outstanding demand. Section 245 permits eligible income tax authorities to set off a refund against an outstanding amount after giving the taxpayer written intimation of the proposed action.

Example

Suppose:

Current year’s refund: ₹65,000

Old outstanding demand: ₹20,000

The department may propose to adjust ₹20,000 against the old demand and issue the balance refund, subject to the applicable process.

However, the old demand may sometimes be incorrect because of:

TDS mismatch;
tax payment not given credit;
rectification pending;
appeal effect not given;
duplicate demand; or
earlier return-processing error.

Therefore, verify the outstanding demand before agreeing with the adjustment.

7. Reassessment Notice – Sections 148A and 148

A reassessment proceeding is more serious. It may arise where the Income Tax Department has information suggesting that income chargeable to tax has escaped assessment. Depending on the applicable law and circumstances, proceedings may involve a show-cause opportunity and reassessment notice.

For older assessment years governed by the Income-tax Act, 1961, Sections 147, 148, 148A and 149 form part of the reassessment framework. The Income-tax Act, 2025 has introduced corresponding provisions under a new section-numbering structure for the new Act framework.

Examples that may result in reassessment-related proceedings include:

undisclosed property transactions;
undisclosed capital gains;
substantial unreported bank deposits;
foreign income not disclosed;
income appearing in third-party information but not reported in ITR; or
other information suggesting income escaped assessment.

Because reassessment proceedings can have substantial tax and penalty implications, taxpayers should obtain professional advice before submitting a response.

Difference Between 143(1) and 143(2)

Taxpayers frequently confuse these two sections.

Particulars	Section 143(1)	Section 143(2)
Nature	Processing/intimation	Scrutiny notice
Issued for	Processing the return and permitted adjustments	Detailed examination of return
Scrutiny involved?	Normally no detailed scrutiny	Yes
Documents required?	Usually limited unless adjustment needs response	Supporting documents may be required
Should you worry?	Review carefully, but it may be routine	Take seriously and prepare a proper response

Therefore, a Section 143(1) intimation should not automatically be described as an income tax scrutiny notice.

How to Check Whether an Income Tax Notice Is Genuine

Fraudulent emails and messages using the name of the Income Tax Department are also possible. Therefore, never make a tax payment merely because you receive an unfamiliar email, SMS or WhatsApp message.

Instead:

Log in directly to the official Income Tax e-Filing portal.
Check Pending Actions / e-Proceedings.
Download the notice from the portal.
Verify the assessment year, PAN and notice details.
Check the Document Identification Number (DIN), where applicable.
Do not click suspicious payment links received through unknown messages.

The Income Tax Department confirms that notices, intimations and letters available for response can be accessed through the e-Proceedings facility on the portal.

What Should You Do Immediately After Receiving an Income Tax Notice?

Do not panic, but do not delay either.

Follow these steps.

Step 1: Read the Complete Notice

Do not rely only on the email subject line.

Download and read the complete notice.

Step 2: Identify the Section

Check whether it is issued under:

Section 139(9);
Section 143(1);
Section 143(2);
Section 142(1);
Section 245;
Section 148/148A; or
another provision.

The correct response depends heavily on the section.

Step 3: Check the Assessment Year

A notice may relate to an earlier financial year rather than the return you have just filed.

Step 4: Check the Response Deadline

Every notice may have a specified compliance date. Missing the deadline can complicate the case significantly.

Step 5: Compare the Notice With Your Records

Review:

filed ITR;
Form 26AS;
AIS/TIS;
Form 16;
Form 16A;
bank statements;
books of account;
capital gain statements;
property documents; and
tax payment challans.

Step 6: Prepare a Point-Wise Response

If the notice contains five questions, answer all five separately. Do not send a generic one-paragraph reply.

Step 7: Attach Relevant Evidence

Supporting evidence strengthens the response. However, avoid uploading irrelevant documents.

Step 8: Submit Through the Correct Portal Facility

Most electronic notices can be viewed and responded to through the Income Tax e-Filing portal’s e-Proceedings facility.

Step 9: Save the Acknowledgement

After submitting the response, save:

response acknowledgement;
uploaded documents;
submission date;
notice copy; and
final response.

These records may be required later.

Common Mistakes While Replying to an Income Tax Notice

Taxpayers often make the situation worse by responding incorrectly. Avoid these mistakes:

Ignoring the Notice

The department will not assume that no reply means there is no problem.

Replying Without Understanding the Section

Different notices require different responses.

Agreeing With an Incorrect Demand

Always reconcile the tax demand before accepting it.

Submitting Incomplete Documents

Missing supporting evidence can weaken your explanation.

Giving Contradictory Explanations

Ensure that your written explanation agrees with the ITR, bank records, books of account and other evidence.

Uploading Documents Without Explanation

Documents alone may not explain your position. Provide a short point-wise written submission.

Waiting Until the Last Day

Technical issues or portal problems can arise. Prepare the response well before the deadline.

Can You Revise Your ITR After Receiving a Notice?

It depends on:

the type of notice;
the assessment year;
whether the statutory time limit for revised return is still available; and
whether the return has already been processed.

For example, in the case of a defective return, the Income Tax Department states that where the time for filing a fresh/revised return is still available, the taxpayer may have that option; otherwise, the taxpayer must respond to the defective-return notice as applicable. Therefore, never assume that filing a revised ITR is the correct solution to every notice.

Do You Need a CA to Reply to an Income Tax Notice?

Not every notice requires extensive professional representation. For example, a simple Section 139(9) defect may sometimes be corrected relatively easily.

However, professional assistance can be particularly useful where the notice involves:

scrutiny under Section 143(2);
detailed information request under Section 142(1);
large tax demand;
capital gains;
unexplained cash or bank deposits;
business income;
foreign income or assets;
multiple years;
reassessment proceedings;
property transactions; or
complicated TDS/AIS mismatches.

A Chartered Accountant can review the ITR, reconcile the available information, identify the actual issue and prepare a properly supported response. For taxpayers and businesses in Greater Noida, taking professional assistance at the beginning of the proceeding can often prevent small reporting discrepancies from becoming larger compliance issues.

Conclusion

Receiving an Income Tax Notice after filing ITR does not necessarily mean that something is seriously wrong. Many communications arise because of reporting mismatches, missing information, processing adjustments or routine verification.

However, every notice should be taken seriously. The most important things are to:

identify the section under which the notice has been issued;
understand why it has been issued;
check the response deadline;
reconcile the information with your ITR, AIS and Form 26AS;
collect supporting documents;
prepare a clear point-wise response; and
submit the response within the prescribed time.

Above all, never ignore an Income Tax Department notice. A timely and properly documented response can often resolve the matter efficiently and prevent unnecessary tax demands, interest, penalties or prolonged proceedings.

Frequently Asked Questions (FAQs)

1. Why did I receive an income tax notice after filing my ITR?

You may receive a notice because of an AIS or Form 26AS mismatch, incorrect ITR form, unreported income, incorrect deduction, TDS mismatch, high-value transaction, scrutiny selection or another issue identified during processing or assessment.

2. Does receiving an income tax notice mean I have done something wrong?

No. A notice does not automatically mean tax evasion or wrongdoing. Some notices simply ask for correction, clarification or supporting information.

3. What is a Section 139(9) notice?

It is a defective-return notice. It indicates that the department has identified incomplete or inconsistent information in the filed return.

4. How much time do I get to reply to a defective ITR notice?

The Income Tax Department generally provides 15 days from receipt of the notice or the period mentioned in the notice, subject to the applicable procedure and any permitted extension.

5. Is Section 143(1) an income tax scrutiny notice?

No. Section 143(1) generally relates to processing of the ITR and communication of the resulting computation. A scrutiny notice is generally issued under Section 143(2).

6. What is a Section 143(2) notice?

It means that the return has been selected for scrutiny and the department may ask the taxpayer to substantiate income, deductions, losses or other claims made in the ITR.

7. Can I ignore an income tax notice if I believe my ITR is correct?

No. Even where your return is correct, submit an appropriate response explaining your position along with supporting documents where required.

8. Can the Income Tax Department adjust my refund against an old demand?

Yes. Subject to the applicable provisions, Section 245 permits adjustment of an income tax refund against an outstanding demand after intimation of the proposed action.

9. Where can I check an income tax notice online?

Log in to the official Income Tax e-Filing portal and check Dashboard → Pending Actions → e-Proceedings for applicable communications.

10. Can I reply to an income tax notice myself?

Yes, depending on the notice. However, for scrutiny, reassessment, large tax demands, business cases, capital gains or complex mismatches, professional assistance from a Chartered Accountant or tax professional may be advisable.

11. What happens if I do not reply to an income tax notice?

The consequences depend on the notice. They may include adverse processing, an invalid return in certain defective-return cases, tax demand, loss of certain benefits or further assessment proceedings.

12. What documents should I keep after replying?

Keep the notice, submitted response, supporting attachments, acknowledgement and any subsequent communication or order issued by the department.