Fighters from the March 23 movement in the Democratic Republic of Congo abandoned Goma, the provincial capital of North Kivu, after seizing control of the city in mid-November.
U.N. spokesman Martin Nesirky said investigators documented hundreds of rapes and at least two killings during recent DRC clashes.
"The U.N. mission (in DRC) is supporting the military justice procedure in conducting thorough investigations into these allegations to ensure that the perpetrators are identified and held accountable," he said in a statement.
U.N. peacekeeping officials in the area said there were reports of M23 rebels in the area, though they weren't present in significant numbers.
The International Criminal Court this week acquitted a Congolese warlord on war crimes charges stemming from conflict in the 2000s. When rebel forces seized Goma in mid-November, the ICC called for the arrest of M23 leaders.
The U.N. High Commissioner for Refugees said as many as 177,000 people were driven from their homes during fighting in eastern DRC.