The ambush took place at Heirok Melei Lampak Chinglon in Thoubal district in the afternoon, 38 km from state capital Imphal.
Superintendent of Police, Thoubal, Radhasyhyam, said the BSF personnel belonging to 54 Battalion, D Company, also retaliated and the gun battle went on for at least half an hour.
No casualty occurred on the side of BSF personnel, the SP said.
Later, additional Manipur police commandos were rushed to the ambush site but the suspected militants had already fled the area, the officer said.
Three weeks ago, suspected armed cadres of NSCN (IM) had assaulted eleven labourers at the ambush site.