KPA President Tongmang Haokip said the party had lent support to the BJP on the condition that interests of the Kuki community would be protected, but that did not happen.
The crackdown comes days after Assam Chief Minister Himanta Biswa Sarma called out the use of the state as a corridor by Rohingyas to go to Delhi, Jammu and Kashmir.
According to the FIR, two tribal women belonging to the Kangpokpi area of Manipur were allegedly abducted, gang-raped and murdered at their workplace by a mob on May 5.
Assam Chief Minister Himanta Biswa Sarma on Tuesday said 133 people from West Bengal have taken shelter in the state, fearing for their lives because of the poll violence back home.