The International Committee of the Red Cross said Wednesday it was growing concerned about the status of civilians in Jonglei.
Five members of a U.N. peacekeeping mission in South Sudan were killed in April while on patrol on Jonglei, the country's largest state. The attack followed a report from the United Nations investigating violence that killed at least 85 people in the state in early 2013 when gangs attacked cattle grazers.
Adrian Zimmerman, deputy director of regional operations for the ICRC, said "thousands of people" were forced to flee ongoing violence in the state. The coming rainy season only added to the humanitarian challenge.
"We are worried about the humanitarian situation in Jonglei state, where continuing violence has forced thousands of civilians to flee their homes," he said in a statement.
Zimmerman said the ICRC was able to identify basic needs in the area, but access was a problem because of security and logistical concerns.
The Sudanese government this week said it agreed to African Union mediation on outstanding issues with South Sudan. Border fighting, ethnic clashes and disputes over oil are threatening to unravel a peace deal that secured South Sudan's independence in 2011.