Up to 60,000 people have fled South Sudan since violence escalated over the past three weeks, the United Nations refugee agency UNHCR said.

An already shaky 2015 peace deal signed after a bloody civil war in the world's newest nation looks uncertain as clashes rage on between troops loyal to President Salva Kiir and those allied with former rebel leader Riek Machar.

"They brought to us very disturbing reports. Armed groups operating on roads to Uganda are preventing people from fleeing," UNHCR spokeswoman Melissa Fleming told a briefing on Tuesday.

"Armed groups are looting villages, murdering civilians and forcibly recruiting young men and boys into their ranks."

The bulk headed to neighbouring Uganda, doubling the flow over that border over the past 10 days, and the rest to Sudan and Kenya, the agency added.

UN: South Sudan refugees could soon hit one million

South Sudan was founded with optimistic celebrations in the capital on July 9, 2011, after it gained independence from Sudan in a referendum that passed with nearly 100 percent of the vote.

The country descended into conflict in December 2013 after Kiir accused Machar of plotting a coup.

Civil war broke out when soldiers from Kiir's Dinka ethnic group disarmed and targeted troops of Machar's Nuer ethnic group.

Machar and commanders loyal to him fled to the countryside, and tens of thousands of people died in the conflict that followed. Many civilians also starved.

The pair of rivals signed a peace agreement late last year, under which Machar was once again made vice president.

The latest setbacks are putting the fragile peace plan at risk.

Renewed clashes

At least nine people were killed over the weekend in renewed clashes between troops loyal to Kiir and troops loyal to Machar, a spokesman for Machar said on Monday.

Government military spokesman Lul Ruai Koang downplayed the weekend clashes, saying there was "small fighting" between the security forces and Machar's supporters.

"We engaged them and they tried to put up some resistance, but at the end we overcame them and they fled to different locations," Koang said.

Koang accused Machar's SPLM/A (IO) party of shelling government positions in Nasir town in Upper Nile state, while the opposition claimed it was the Sudan People's Liberation Army (SPLA) that shelled their positions.

The United States said over the weekend it had received "disturbing reports" of renewed violence in the south of the country and the United Nations is considering imposing an arms embargo.