Attacks at a mosque, a church and a hospital came after the rebels seized the oil hub of Bentiu, the statement said, noting hate speech, including demands that certain groups leave town and the urging of men to rape women, were heard in local radio broadcasts.
About 200 were killed at the Kali-Balleee mosque, and Nuer who attempted to hide, instead of cheer the rebels as they entered Bantiu, were also killed.
The U.N. Mission added an attack last week on one of its bases in the town of Bor, which killed 58 people, could constitute a war crime.
Fighting broke out last year after South Sudan President Salva Kiir, a member of the dominant Dinka tribe, accused his vice president, Riek Machar of attempting a coup. The Nuer community is seen as supporters of Machar.
The United Nations has about 8,500 peacekeepers stationed in South Sudan.