Pakistani Information Minister Shiekh Rashid Ahmed confirmed the arrest of Abu Farraj al-Libbi.
"We arrested [him] yesterday with four other people," said Shiekh Rashid Ahmed.
The Libyan native, considered third in charge of al-Qaida, had a $1 million bounty on his head.
He is one of the group's top operational commanders, and is accused of planning two unsuccessful bomb attacks against Pakistan's president, Pervez Musharraf, in 2003.
Mr. Rashid would not comment on where the suspect was arrested, but he was thought to have been hiding in Pakistan's northern tribal areas.