The United Nations mission in South Sudan has condemned what it called "the targeted killings of civilians based on their ethnic origins and nationality" in a disputed town that is under the control of anti-government forces.

In Bentiu, the capital of oil-producing Unity state, more than 200 people sheltering inside a mosque were killed last week after rebel forces seized the key town, the mission said in a statement, describing an apparent massacre after government troops were ousted.

Individuals "associated with the opposition" had used an FM radio station to broadcast hate speech, even urging "men from one community to commit vengeful sexual violence against women from another community", it said.

After rebel forces captured Bentiu last Tuesday, "they searched a number of places where hundreds of South Sudanese and foreign civilians had taken refuge and killed hundreds of the civilians after determining their ethnicity or nationality", the statement said, citing the accounts of UN human rights investigators on the ground.

At Bentiu hospital, several men, women and children from the Nuer ethnic group were killed after hiding and refusing to join other Nuers who had come out to cheer the rebels as they seized the town.

Individuals from other South Sudanese communities – as well as people from Darfur – were specifically targeted and killed at the hospital, the statement said. Hundreds more people, who were sheltering at a mosque and a Catholic church, were killed or wounded.

Toby Lanzer, the UN's top humanitarian official in South Sudan, said in Twitter posts on Sunday that there were shocking scenes of atrocities, with "bodies of people executed" lying in the streets of Bentiu.

Thousands of people have been killed in violence since December, when presidential guards splintered and fought along ethnic lines. The violence later spread across the country as soldiers loyal to President Salva Kiir tried to put down a rebellion led by Riek Machar, the former vice-president.

The UN has been warning of mounting evidence of ethnically- targeted killings in the world's newest nation as both government troops and rebel forces lose and gain territories in sporadic clashes. Despite a ceasefire signed earlier this year, both sides continue to trade allegations over rights violations and civilian abuses.

Machar, an ethnic Nuer, has said he wants to see the exit of Kiir, an ethnic Dinka whom he accuses of acting like a dictator.

Kiir accuses Machar of launching a failed coup attempt in December 2013 that the government says sparked unrest across the country.

Peace talks in neighbouring Ethiopia have proceeded slowly.