A 15-member team of the Anti-Corruption Bureau led by Superintendent of Police Raunaq Ali Hazarika began the raid at 9 am at the residence of the accused located in Tarun Nagar area of the city here.
Hazarika said some documents were seized from the residence and the raid was still continuing.
Khan, currently lodged in the Guwahati Central Jail, was arrested in 2009 after the multi-crore scam of diversion of development fund, allotted to the N C Hills Autonomous Council, to militant outfit Dima Halam Daogah (Jewel faction) came to light.
The scam was investigated by the National Investigating Agency (NIA) and it subsequently filed a chargesheet in connection with this case.
The case was later handed over to the CBI which arrested Khan, then an official of the state Social Welfare Department.
Raids were also conducted earlier in the various residences of Khan and his relatives with huge amounts of cash, jewellery and documents recovered.
In a particular raid, huge amounts of cash amounting to several crores of Rupees was found hidden within the walls of Khan's residence.