Protests began Monday in western South Sudan, where youth movements have expressed frustration with the political state of affairs. Tensions escalated when state officials tried to move the seat of local government to a nearby town.
One witness told the independent Sudan Tribune that riot police opened fire on demonstrators, killing four people.
The U.N peacekeeping mission in South Sudan deployed to the regional airport to provide security. Peacekeepers said they saw about 300 youths armed with machetes demonstrating in the streets.
Kieran Dwyer, a spokesman for the U.N. Department of Peacekeeping Operations, told the U.N. News Center that "around 5,000 civilians" have sought refuge in U.N. camps.
The violence follows reports that Sudan and South Sudan reached a deal to set up a demilitarized zone along their shared border. South Sudan's independence last year has been complicated by ethnic rivalries, oil disputes and border clashes. Independence was gained through am agreement that ended the region's long civil war.