Income Tax Portal Updates Link Aadhaar Manual for Income Tax Act, 2025: What Taxpayers Need to Know

The Income Tax Department's e-Filing portal has updated its Link Aadhaar User Manual for the Income Tax Act, 2025, which has applied from 1 April 2026. The manual now cites section 262 of the Income Tax Act, 2025 alongside section 139AA of the Income-tax Act, 1961, the earlier provision on PAN-Aadhaar linking. For practitioners handling linking requests, the main practical change is in the payment step: the delayed-linking fee is now paid by choosing the 2025 Act in the e-Pay Tax flow.

Who has to link

Per the manual, a PAN allotted on or before 1 July 2017 must be linked with Aadhaar unless the holder falls in an exempt category. For new PAN applicants, linking happens automatically during the PAN application. If a person who is required to link does not do so, the PAN becomes inoperative.

The portal's Link Aadhaar help page lists the persons for whom linking is not compulsory:

• individuals residing in Assam, Jammu and Kashmir, and Meghalaya;
• non-residents;
• individuals aged 80 years or more during the previous year;
• persons who are not citizens of India.

What an inoperative PAN costs

The help page sets out the consequences: no refund of tax due is made, no interest is paid on such refund, TDS is deducted at a higher rate and TCS is collected at a higher rate. The page refers to the 1961 Act sections for the higher rates (206AA for TDS and 206CC for TCS). The fee for delayed linking, which also applies to making an inoperative PAN operative again by intimating Aadhaar, is Rs 1,000.

Step 1: pay the fee

The fee is paid through e-Pay Tax on the portal. Under the updated flow, the taxpayer selects the Income Tax Act, 2025, the relevant tax year, payment type "Other Receipts (500)" and the sub-type "Fee for delay in Linking Pan with Aadhaar". The amount is pre-filled before the challan is generated. If the fee has already been paid but does not yet show in the linking flow, the manual says to wait 4 to 5 working days before submitting the linking request.

Step 2: submit the linking request

The request can be made before or after login. Before login, use Link Aadhaar under Quick Links on the e-Filing home page. After login, go to the Profile section on the dashboard. The prerequisites are a valid PAN, the Aadhaar number and a valid mobile number for OTP. The system validates PAN and Aadhaar, checks for the fee payment and, if the payment is found, lets the user complete the request with OTP validation.

Mismatches and status checks

If the Aadhaar is already linked to another PAN, or the PAN to another Aadhaar, the manual tells the taxpayer to contact the Jurisdictional Assessing Officer and request delinking before the correct link can be made. Status can be checked through Link Aadhaar Status before or after login by entering PAN and Aadhaar. A successful request shows a confirmation; a pending one shows that validation is in progress with UIDAI.

Practical points for professionals

• In e-Pay Tax, check the Act, tax year, payment type and sub-type before generating the challan.
• Allow 4 to 5 working days for the challan to reflect before retrying.
• Do not treat payment as completion. Confirm the final status on the portal and keep the confirmation on file, since an inoperative PAN affects refunds and TDS/TCS rates.
• For clients in an exempt category, record the basis of exemption instead of paying the fee.

Updated on 27 September 2026: linked the e-Filing portal's Link Aadhaar manual and help page, added the exempt categories, the Rs 1,000 fee, the consequences of an inoperative PAN and the payment sub-type.