Thousands of heavily armed gunmen from rival ethnic groups have been fighting for almost two weeks in the impoverished region, while government troops and UN peacekeepers have said their forces are unable to intervene as they would be overwhelmed.
Doctors Without Borders (MSF - Medecins Sans Frontieres) said that their "teams on the ground have treated hundreds of wounded and are attempting to reach out to thousands more hiding in the bush".
"We are expecting more people still to come," MSF chief Raphael Gorgeu said.
UN humanitarian chief Valerie Amos, in a statement in New York, said she was "alarmed by the deteriorating humanitarian situation in Pibor county in Jonglei, where an estimated 100,000 civilians have been cut off from life-saving assistance as a result of fighting".
Lou Nuer gunmen from northern Jonglei have marched south towards Pibor, an area of their rivals, the Murle.
Previous such attacks in the troubled eastern region have seen hundreds -- if not thousands -- of civilians killed.
In earlier clashes, rights groups accused all sides of abusing and raping civilians.
"The fighting is threatening the lives of ordinary people and has reduced the ability of humanitarian organisations to provide urgently needed help," Amos said.
The reports echo attacks in December 2011, when some 8,000 Lou Nuer marched south killing and looting in what they said were reprisals for earlier attacks and cattle raids by Murle fighters.
The United Nations later estimated that more than 600 people were massacred, although local officials reported the figure to have been far higher.
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