A five-member group of the KPLT came face-to-face with the security forces at Deothar in Bokajan subdivision and fired at them, police said.
After heavy exchange of fire, the c-in-c, Apang Ingti, was shot dead at around 4 am, while another cadre identified as Soban was injured and apprehended, the police said.
The rest of the three ultras fled away. An AK-47 and a huge quantity of ammunition were recovered from the militants, the police said.
Ingti was wanted in connection with killings, kidnappings and extortion in the district. The KPLT is the breakaway group of militant Karbi Longri National Liberation Front after it declared unilateral ceasefire on February 10 last year.