Acting on a tip-off, a joint team of police and army launched an operation in Morabari jungle in the district and arrested the duo.
The NDFB(S) commander has been identified as Rabi Basumatary alias Rongabaja and his personal bodyguard as Jwnglaw Narzary alias Jekhai, BTAD IGP L R Bishnoi said.
An AK-56 rifle, 170 rounds of AK ammunitions, 50 rounds of INSAS ammunitions and four hand grenades were seized from their possession.
Basumatary was allegedly involved in the killing of the then inspector-in-charge of Rupsi outpost in Kokrajhar district, Narayan Barman, on September 26, 2013.