This is the first time the United Nations has directly suggested that government forces dug the mass graves.
Gunfire and explosions erupted in Congo’s eastern city of Bukavu, witnesses said, as Congolese troops clashed with those loyal to a renegade colonel.
A Democratic Republic of Congo army spokesperson for South Kivu region, Dieudonne Kasereka, told Al Jazeera clashes started after police came to disarm Colonel Abbas Kayonga, who was sacked from his post on Thursday.
Security has deteriorated across DRC since the end of last year, when President Joseph Kabila refused to step down despite his mandate expiring.
Surging militia violence in the east – which for decades has been a tinderbox of ethnic rivalries fuelled by the region’s mineral wealth – and in the formerly peaceful central Kasai region have raised fears the country could slip back to the multi-faceted civil wars of the turn of the century.
Those wars killed hundreds of thousands of people while millions of others are thought to have died of hunger and disease.
Kayonga is a former rebel from a group that was successfully disarmed and integrated into the Congolese military.
“We are determined to arrest him and make him face justice,” Kasereka said.
Two security sources estimated the size of Kayonga’s faction at about 40 men.
The national electoral commission was expected to announce a date for the election to replace Kabila later on Sunday. Last month, it said the vote cannot take place until April 2019, raising fears of an escalation in violence and civil disturbances.
US envoy Nikki Haley, after meeting with Kabila last month, said the vote must happen in 2018 or Congo will lose international support.