Qari Ahrar, an employee of the Civil Aviation Authority (CAA), led a public 'dua' (prayer) for the Taliban to emerge victorious during his weekly Friday sermon in the CAA staff colony mosque here last week, police said.
His arrest came days after the government's announcement that religious leaders should avoid extolling militants.
The government also announced to register mosques and clerics and avoid the misuse of sound system.
Pakistan has increased punitive measures against people involved in spreading extremism after the December 16 Peshawar school massacre that left 150 people dead, including 136 students.