Friday's operation in the Kahozi-Biega park, the only place in the world where the Grauer's gorilla roam in the wild, also saw around 90 huts torched.
Congloese authorities accuse militia groups of illegal mining in the area and using local Pygmies as a cover.
"In a joint operation with the Armed Forces of the Democratic Republic of Congo (FARDC) and forest guards to evict the Pygmies... two Pygmies were killed and others were wounded," said Pascal Cimana, the top official of the adjoining Kalehe region.
"At least 87 mud huts were burnt. In this place the Raia Mutomboki and CRND (National Council for Rebirth and Democracy) armed groups were engaged in mining," Cimana said.
Army spokesman Major Louis Tshiamwang said six members of the CRND militia -- an offshoot of a Rwandan Hutu group -- and two pygmies were killed.
An estimated 120 militia groups operate in the mineral-rich eastern DRC, many of them a legacy of two regional wars from 1996 to 2003.
The conflict has claimed hundreds of civilian lives this year alone.
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