By Michelle Nichols
UNITED NATIONS, April 21 (Reuters) - Rebels slaughtered hundreds of civilians when they seized the South Sudan oil hub of Bentiu, hunting down men, women and children who had sought refuge in a hospital, mosque and Catholic church, the United Nations said on Monday.
Rebel troops overran Bentiu, the capital of the oil producing Unity State, on Tuesday. More than 1 million people have fled their homes since fighting erupted in the world's youngest country in December between troops backing President Salva Kiir and soldiers loyal to his sacked vice president, Riek Machar.
The fighting has exacerbated ethnic tensions between Kiir's Dinka people and Machar's Nuer.
The U.N. peacekeeping mission in South Sudan said that its human rights investigators confirmed that rebels "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 U.N. mission, known as UNMISS, strongly condemned the targeted killings on April 15-16 and the use of Radio Bentiu FM to broadcast hate speech.
While some rebel commanders broadcast calls for unity, "others broadcast hate messages declaring that certain ethnic groups should not stay in Bentiu and even calling on men from one community to commit vengeful sexual violence against women from another community," UNMISS said in a statement.
At Bentiu hospital, Nuer men, women and children were killed for hiding and not joining other Nuers in cheering the rebels as they entered the town. People from other South Sudanese communities and from Darfur in Sudan were also targeted and killed, the United Nations said.
Rebels also entered the Kali-Ballee Mosque, a Catholic church and an empty World Food Program compound where civilians had sought refuge and separated them by nationalities and ethnicities - escorting some to safety and killing others.
"More than 200 civilians were reportedly killed and over 400 wounded at the mosque," the U.N. mission said.
U.N. peacekeepers rescued more than 500 civilians from Bentiu hospital and other places and escorted thousands more as they walked to the U.N. base. The U.N. said it is currently protecting more than 12,000 civilians at its Bentiu base.
Around the country the United Nations is protecting tens of thousands of civilians who have sought refuge at its bases.
After the rebels seized Bentiu, Dinka residents of Bor town in Jonglei state attacked a U.N. base on Thursday where about 5,000 people, mostly Nuer, were sheltering. The mob of armed civilians pretended to be peaceful protesters delivering a petition to the United Nations before opening fire in the base.
Some 58 people were killed and another 98 injured, including two Indian peacekeepers, the U.N. mission said.
On Jan. 23, the warring parties in South Sudan agreed to a cessation of hostilities but fighting has continued in parts of South Sudan, which seceded from Sudan in 2011 under an agreement to end decades of war.
The current conflict has disrupted oil production, which provides a hefty portion of the government's revenue. After seizing Bentiu, the rebels warned oil firms to pack up and leave within a week.
(Reporting by Michelle Nichols; Editing by Tom Brown)