The investigative mission this month found the latest mass graves in the Diboko and Sumbula areas of the Kamonia territory, the UN said.
The violence began last year when Kamwina Nsapu, a tribal chieftain in territory near the southern border with Angola, openly challenged the authority of President Joseph Kabila's government, provoking a crackdown by security forces.
Nsapu was killed in a police operation in August 2016, but his armed followers fight on in the belief he is still alive, because he was buried by the regime without respect for traditional rites accorded leaders of his stature which would have opened the way to a rightful succession.
Last February, MONUSCO accused the Kamwina Nsapu militia of "atrocities... including the recruiting and use of child soldiers," but also condemned "a disproportionate use of force" by government troops.
Two western experts sent to investigate the conflict by UN Secretary-General Antonio Guterres went missing in March and their bodies were found in a shallow grave by peacekeepers a fortnight later.
The government blamed the tribal militia for their murders.