Waiting For ITR Refund? Tax Dept Flags Form 16 Errors & Pauses Payments

Waiting For ITR Refund? Tax Dept Flags Form 16 Errors & Pauses Payments

Many salaried taxpayers have not received their ITR refunds for AY 2025–26 due to mismatches between claims in their returns and employer data in Form 16. The Income Tax Department has paused refunds temporarily and advised taxpayers to correct errors or respond promptly to emails.

Manoj YadavUpdated: Wednesday, December 24, 2025, 11:43 AM IST
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Income tax refunds are delayed this year due to heightened scrutiny of high-value claims. |

New Delhi: A large number of salaried taxpayers have not received their income tax refunds for the Assessment Year 2025–26. The Income Tax Department has clarified that this delay is not due to any technical issue or system failure. Instead, refunds have been put on hold because of mismatches between the claims made in income tax returns (ITR) and salary details provided by employers in Form 16.

According to the department, when figures mentioned in ITRs do not match Form 16 (Annexure II), refunds are temporarily stopped.

What the Income Tax Department Is Saying?

The department has been sending emails directly to affected taxpayers. These emails clearly mention that exemptions or deductions claimed in the ITR do not match the salary data submitted by the employer. Due to this mismatch, the refund amount appears unusually high, and the system has flagged such returns under internal risk checks.

Officials have stressed that the refund has not been cancelled, only paused until the issue is resolved.

Refund Is Delayed, Not Cancelled

Tax experts have reassured taxpayers that there is no need to panic. The refund has only been stopped temporarily. Once the taxpayer corrects the mismatch or submits a proper response, the refund process can continue.

Common Reasons for Mismatch

Most problems are linked to salary-related tax benefits. These include claiming HRA when it is not reflected in Form 16, claiming LTA or other allowances not included by the employer, or claiming deductions that are not present in company records. Due to this, the system assumes the refund is overstated and holds the return for review.

Ignoring Emails Can Cause Trouble

The Income Tax Department has warned that ignoring such emails may be seen as negligence. This could lead to the case being selected for detailed scrutiny later.

Revised Return Deadline Matters

For AY 2025–26, taxpayers can file a revised return until December 31, 2025, without extra tax or penalty. If missed, an updated return will have to be filed from January 1, 2026, which may attract penalties.

What Taxpayers Should Do Now?

Taxpayers who receive emails should log in to the e-filing portal and compare their ITR with Form 16 and Form 26AS. If the claim is correct, they can respond confidently. If a mistake is found, filing a revised return quickly is the safest option.

Experts say timely action can clear the path for the refund.

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