Mullah Hakim Latifi, who has often claimed responsibility for attacks against U.S.-led coalition forces, was caught in southwestern Baluchistan province, Information Minister Sheikh Rashid Ahmed said.
Baluchistan borders Afghanistan, and members of the Taliban are believed to have sought refuge in the area, the AP reports.
Interior Minister Aftab Khan Sherpao confirmed the arrest. Another interior ministry official said Latifi had been using a Pakistani cellular phone and would be moved to Islamabad, the Pakistani capital, for questioning.
The arrest came less than a week after Afghan President Hamid Karzai praised Pakistan for helping Afghanistan hold peaceful legislative elections on Sept. 18. Pakistan had deployed additional troops to prevent Taliban and al-Qaida fighters from crossing the border into Afghanistan and disrupting the election.
Rebels are active in the volatile south and east of Afghanistan, and have stepped up attacks this year. More than 1,300 people, including hundreds of militants, have died in the past seven months.
Pakistan was once a supporter of the Taliban, but withdrew its support and became a chief ally of the U.S.-led coalition forces that ousted the militia. AM