Dr Shakil Afridi was shifted from Peshawar Jail to an undisclosed prison in another city, jail sources informed.
Dr Afridi is sentenced to 33 years for involvement in anti-state activities by a tribal court in 2012. The tribal court alleged that Afridi paid two million rupees to a militant group and helped to provide medical assistance to militant commanders in Khyber.
Afridi was arrested after US troops killed Al Qaeda chief bin Laden in the Pakistani town of Abbottabad in May 2011. Islamabad branded the raid a violation of sovereignty, and Pakistan's relations with the US fell to an all-time low.