Anura Senanayake, the then deputy inspector general in charge of capital Colombo was arrested following a Crime Investigations Department questioning.
He is accused of subverting the investigation in order to portray it as a road accident.
An officer in charge of a police station is already in remand custody in the same case.
Thajudeen's body was found inside a charred car at Park Road, south Colombo in May 2012. The police had earlier claimed that the former Sri Lankan Rugby captain burnt to death in a road accident.
After President Maithripala Sirisena came to power last year, police reopened the case. Thajudeen's body was exhumed for a fresh autopsy.
Thajudeen's murder has been linked to the sons of the former President Rajapaksa.
Rajapaksa family is embroiled in many cases since the defeat of the former President in the January 2015 election.
