An FIR was registered against Khan, a former Islamabad police chief, on Monday for kidnapping Inspector Rana Pervez.
Pervez and revenue official Arshad Mehmood were reported missing on December 3, 2010. A suspect was arrested last month for his alleged involvement in the kidnapping.
The suspect, Raja Munir, is considered to be an associate of Asmatullah Muavia, a commander of the Punjabi Taliban.
In April 2011, the police had arrested Muavia's brother Sibghatullah from Vehari in Punjab for his alleged involvement in the kidnapping.
The Supreme Court had earlier expressed concern over the alleged links of police officials with militants.
The apex court had clubbed the kidnapping case with the larger case of "missing persons" or those detained without charge by security agencies and asked police to register an FIR against those responsible, Express Tribune reported.
The apex court warned the government yesterday that it would face action if it fails to produce 33 "missing persons" believed to be in the custody of security forces by December 5.
