The first body, unearthed over the weekend, wore the standard ochre robe of the Ashaninka, said Ivan Rivasplata, leader of the forensic anthropologists from the Peruvian prosecutor's office engaged in the mission with army escorts.
He said in Lima that the team hopes to exhume about 130 bodies from five common graves in two communities in the Apurimac, Ene and Mantaro river valleys, where remnants of the Shining Path continue to exert influence, living off a vibrant cocaine trade.
The entire ethnic group numbers only about 97,000, according to Peru's 2007 census.
The Ashaninka, a hunter-gather people, live primarily in an area where jungle meets mountain. It was there that the Shining Path tried to forge the cradle of a new Maoist-inspired state. Most fiercely resisted the rebels.
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One Ashaninka survivor, Miguel Pachacamac, said in video taken by the forensic team and provided to The Associated Press that rebels did not even bother to bury the natives they killed. "They left them for the vultures."
The valley has also been the site of a bitter struggle over a major hydroelectric project that would have benefited Brazil and Peru, while displacing thousands of people. The Ashaninka, led by tribal activist Ruth Buendia, succeeded in halting it through legal challenges.