Sayed Muhammad Akbar Agha, head of Jaishul Muslimeen (Army of Muslims), was taken into custody in the southern Pakistani port city of Karachi, a senior security official said on Saturday.
"Agha was arrested from a flat in central Karachi early last week," the official said.
Information Minister Shaikh Rashid said Agha was in Pakistani custody, but declined to give details.
The Jaish claimed the abduction of Shqipe Hebibi from Kosovo, Annetta Flanigan of Northern Ireland and Filipino diplomat Angelito Nayan from a busy Kabul street on 28 October.
The trio, who were overseeing Afghanistan's first presidential elections in October, were released unharmed on 23 November after prolonged negotiations between representatives of the Afghan government and the group during which the abductors set several deadlines threatening to kill the hostages.
The Afghan government said no agreement was reached with the abductors and no ransom was paid for the freedom of the UN hostages.
Agha has told interrogators he slipped across the border into southwestern Pakistan from where he managed to reach Karachi, the official said.