Jundullah commander Abdul Salam Rigi was arrested near provincial capital Quetta, the officials said.
"He was arrested during a security check near the Lok Pas area on the outskirts of Quetta on Sunday morning," said an official.
Rigi was held when he was coming from the Iranian town of Taftan to Quetta on a bus, he said adding that the militant commander has been taken to an undisclosed place for questioning.
Rigi was the senior most commander of Jundullah after the capture and subsequent execution of the group's former chief Abdul Malek Rigi by the Iranian government in 2010.
The official said Rigi is suspected of carrying out bomb attacks in Pakistan and Iran.
Balochistan Home Secretary Akbar Hussain Durrani confirmed the arrest of a "suspect" but did not say he was Abdul Salam Rigi.
"I can only say he is in custody of security forces and has been taken for questioning," said Durrani.
