The bodies of Paoginlal Hangshing, 20, and Tinginlun Chongloi, 21, were recovered in Kangpokpi district.
A joint operation involving Manipur Police, CRPF, Assam Rifles, CoBRA and RAF was conducted along SP Road.
The recovery follows the killing of three Kuki community members in Noney district and comes amid prolonged ethnic violence in Manipur.