The provincial capital of Bor has become the focus of a bloody power battle between President Salva Kiir and his former vice president Riek Machar that has already left more than 1,000 dead.
UN reconnaissance planes have spotted "large" groups of armed youths and regular troops who have defected from Kiir's side north of Bor, UN spokesman Martin Nesirky told reporters yesterday.
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The number in the UN compound in Bor has fallen from up to 17,000 last week to about 8,000 yesterday, Nesirky said.
"Thousands of civilians have been seen heading south on the road to Juba during the course, motivated one assumes primarily by fears of an assault on Bor by these groups," he added.
The Doctors Without Borders group said that thousands are also arriving from Bor in Awerial in neighboring Lakes state.
Bor is capital of Jonglei state, which has a bitter history of conflict between the ethnic Nuer who mainly follow Machar and the Dinka, Kiir's tribe.
In 1991, an estimated 2,000 people were killed in a massacre in Bor blamed on the Nuer.
Nesirky said the United Nations is "extremely concerned about mounting evidence of gross violations of international human rights laws" across South Sudan.
He said the key oil city of Bentiu remains in the hands of forces loyal to Machar and there were fears that "heavy fighting" in the region could spill over into neighbouring Warap state.
UN leader Ban Ki-moon spoke to Kiir yesterday and called on him to carry out a promise to release political prisoners, a UN statement said.
Ban and Kiir also discussed efforts to reinforce the UN peacekeeping mission in South Sudan following reports that Kiir has objected to troops from some countries.
The government obstacles were discussed in UN Security Council talks on the crisis yesterday, UN peacekeeping chief Herve Ladsous said. The 15-member council has approved sending up to 6,000 extra troops to South Sudan.
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