Income Tax returns filed, yet refunds lag: CA explains what’s causing the delays

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While income-tax refunds are now issued more quickly than ever with improved technology and faster processing systems, this year, numerous taxpayers are still waiting for their return. According to the Income Tax Department's website over 7.57 crore Income Tax Returns (ITRs) were filed for the Assessment Year (AY) 2025-26 as of September 23, 2025. While the numbers look healthy on paper, delays in processing are piling up.

In a recent post on X, CA Abhishek Raja Ram (@abhishekrajaram) outlined several possible causes behind the slow turnaround of ITRs this season.

ITR refunds may be delayed due to departmental backlog, extra scrutiny of old-regime returns, high or doubtful deduction claims, income mismatches, defective returns, or past filing issues. These factors trigger manual verification or hold processing. If details are correct,… pic.twitter.com/Xor3fgdMI1

— Abhishek Raja "Ram" (@abhishekrajaram) November 17, 2025

• The revised ITR-forms (for different categories of taxpayers) (for various types of taxpayers) were not made available to everyone on time, limiting access for many.
• Many taxpayers rely on pre-populated information (such as TDS details), however the site has not correctly uploaded or reconciled this data, resulting in delays.
• Confusion over which form to use: Due to changes in ITR forms, some filers are puzzled whether to use ITR-1, ITR-2, ITR-3, etc., which slows down filing.
• Heavy traffic, particularly as deadlines near, is causing login problems, time-outs, and delayed save or submit features, preventing many from completing the process.

Simply put, despite this strong filing momentum, processing hasn’t kept pace — and that’s where many taxpayers are feeling the pinch.

• Based on your income sources (salary, business, capital gains) confirm the right ITR form and check whether you’re under audit.
• It's better that you reconcile pre-filled data (TDS, salary, interest) with your own records early.
• File before the extended deadline and don’t wait till the last moment.
• As soon as you file, E-verify promptly via Aadhaar OTP, EVC, or net banking.
• Keep documentation ready like digital copies of acknowledgement, submission receipts, and verification proof.
• If audit is involved or your income sources are complex, consult a CA or tax professional.

Meanwhile, it is worth noting that the Central Board of Direct Taxes (CBDT) extended the due date for filing ITRs for certain assessees (under clause (a) of Explanation 2 to section 139(1)) has been pushed out from 31 October 2025 to 10 December 2025.

Additionally, the deadline for audit report submissions (for those under section 44AB) has been extended from 31 October to 10 November 2025.