Adnan Rashid was nabbed from South Waziritan in injured condition after he escaped from a cordon off area of North Waziristan where forces are carrying operation against the local and foreign fighters.
An intelligence official said he was arrested from a house in Wana area on Friday and was shifted in a helicopter to undisclosed location.
The tribal sources also confirmed the arrest but said that the militant was captured from Shakai valley area.
A Taliban commander also rejected it as "mere propaganda" by the army to weaken Taliban.
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However, a tribal source from South Waziristan said that Taliban today distributed a pamphlet in the area and threatened to target rival commander Bhawal Khan for helping the security forces in the arrest of Rashid.
Rashid, a key rebel, was sentenced to death by a military court for attacking Musharraf and was lodged in Bannu district jail near North Waziristan.
He escaped with about 400 militants when rebels stormed the jail in 2012 to release him.
Rashid also made headline when he wrote a letter to teenage activist Malala Yousafzai after she was shot by the militants. He justified that attack but wished that it should not have happened.
He planned the Dera Ismail Khan jailbreak in 2013 which resulted in release of about 250 militants.