The report said hundreds of people including pregnant women and minors were raped in Unity state by soldiers from either side.
Tens of thousands have been killed in the conflict, which started more than two years ago, as government forces battle rebels.
The UN said sexual violence centered in oil-rich Unity, and government soldiers were responsible for most incidents.
At least 35 women were raped by government soldiers in wo months of 2015 outside their base in the Unity capital, Bentiu.