BPF is the ruling party in BTC and an ally of the ruling Congress in Assam since the 2006 assembly elections.
Police claimed to have recovered two AK-47 rifles and ammunition from Brahma's house on Friday during a drive to seize illegal weapons from Bodoland Territorial Areas District. BPF Rajya Sabha member Biswajit Daimary termed Brahma's arrest unfortunate and hinted at a strain in ties with the Congress.
"The arrests of BPF representatives are a matter of concern."
A combative Gogoi responded, "It is up to the BPF to decide whether they want to stay with the Congress or not."
Allegations of the involvement of several BPF leaders in the clashes between multi-faith Bodo tribals and Bengali Muslim migrants have repeatedly surfaced in the recent past.
In July-August, violence between the two groups had claimed 97 lives.