The confidential report, leaked to Reuters agency, says Uganda is also backing the M23 rebels, who have been fighting the DRC's army since April.
The document builds on a UN report published in June which accused Rwanda of supporting the insurgents.
Rwanda and Uganda strenuously deny supporting the rebellion.
The BBC's Barbara Plett, at the UN, says that during the past two decades Rwanda has backed armed groups in the east of DR Congo as a way to fight Hutu rebels who fled there after the genocide of the 1990s.
Some accuse Rwanda of using militias as proxies in an on-going battle for the region, which is rich in minerals, our correspondent adds.