Local people were forced to dispose of the bodies including those of women and children in an open area near the town of western El-Geneina between June 20-21, the UN statement said, Reuters reported.
Some of the people had died from untreated injuries during a wave of violence by the RSF and allied militia in the days following the killing of local governor Khamis Abbakar, it said.
"I condemn in the strongest terms the killing of civilians and hors de combat individuals, and I am further appalled by the callous and disrespectful way the dead, along with their families and communities, were treated," said UN High Commissioner for Human Rights Volker Turk in the same statement.
He called for a prompt and thorough investigation.
It was not immediately clear what portion of the dead were Masalits. Ethnically motivated bloodshed has escalated in recent weeks in step with war between rival military factions that erupted in April.