The report, leaked Thursday by the French newspaper Le Monde, says that Rwanda's President Paul Kagame threatened to withdraw troops from the UN-African peacekeeping mission in Darfur if the genocide allegation was published.
It was not immediately possible to get comment Friday from Rwanda's government.
About 1 million Hutus including perpetrators of Rwanda's 1994 genocide fled to neighboring Congo in the aftermath of the slaughter. Rwandan troops invaded and thousands were slaughtered in UN refugee camps, the report said.
"The extensive use of non-firearms, particularly hammers, and the systematic massacres of survivors after camps were taken prove that the number of deaths cannot be put down to the margins of war," the leaked report says.
The draft from the High Commissioner for Human Rights states that the systematic and widespread attacks "could be classified as crimes of genocide" by a competent court, according to Le Monde.
The Rwandan government says their forces were hunting down perpetrators of the 1994 genocide during which more than half a million people were slaughtered, mostly ethnic Tutsis and moderate Hutus. However, the leaked draft report said most of the Hutu victims in Congo were women and children, along with the sick and the elderly.
The 546-page report, which should be published next week, covers Rwanda's 1996 invasion of Congo, then called Zaire, and a second invasion two years later that exploded into a regional war involving eight countries.
The report says that while Rwanda has permitted large numbers of Hutus to return home, that "does not rule out the intention of destroying part of an ethnic group as such and thus committing a crime of genocide."
The Rwandan president has tried to downplay the role of ethnicity in post-genocide Rwanda, and people in the country rarely refer to themselves as Hutu or Tutsi and can face charges for speaking publicly about ethnicity.