Safar Ali and Mehboob advocate were arrested just before they were to address a press conference in Gilgit.
The BNF, a nationalist party with one seat in the Gilgit-Baltistan Legislative Assembly, has been accused by some of having ties with India's premier intelligence agency Research and Analysis Wing (RAW).
But it is unclear whether these suspicions were behind the arrests.
"We arrested them because we had been ordered to," a police official said when asked why the two men were arrested.
The pair was later shifted to Cantt Police Station for further investigation.
A source privy to the development said the BNF leaders had organised the press conference to clarify their position regarding recent police allegations of sedition and treason.
Police bust RAW-funded ring of saboteurs in G-B
Last month, the police claimed to have arrested members of a RAW-financed network planning to sabotage the China-Pakistan Economic Corridor (CPEC) project.
"We have arrested 12 members of a gang and have also recovered weapons from their possession," said the inspector general of police, adding that 60 other people affiliated with the network had been identified and would be arrested soon.
The IGP at the time had inferred that the gang was linked to the BNF.
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