Mass killings, extrajudicial killings, arbitrary detentions and sexual violence are some of the other violations seen in the country, said UN Assistant Secretary-General for Human Rights Ivan Simonovic.
"Quite a number of child soldiers have been recruited in the so-called White Army," he said, referring to the Nuer tribe's militia fighting in Jonglei state. "We are thoroughly investigating these allegations."
South Sudan's conflict broke out December 15 as a political dispute but quickly broke down along ethnic lines between followers of the president, an ethnic Dinka, and the former vice president, a Nuer.
Simonovic told a news conference that he saw at least 15 dead bodies in Bentiu, in the oil-rich state of Unity, including one man's arms bound behind his back.
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"We have heard and have allegations of a large number of victims bound tied and killed. However I myself have only seen by the road one victim," he said.
Simonovic said an independent and impartial fact-finding commission should be established to investigate the crimes and make those responsible accountable.
In terms of the number dead Simonovic said: "I would not like to be specific in how many thousands but we are talking many thousands.