“Gunshots, heavily armed exchange UN House area once again; going on now since approx. 0825 (0525 GMT),” the UN Mission in South Sudan (UNMISS) said on Twitter.
The UN runs a camp for people uprooted by the war close to where both former rebels and government soldiers are camped.
Residents fled the area as the UN reported the use of mortars, rocket-propelled grenades and “heavy ground assault weaponry”.
A spokesman for former rebel leader turned vice president Riek Machar blamed government troops.
“Our forces have been attacked at Jebel base,” said James Gatdet Dak, who claimed the attack had been repulsed. “We hope it will not escalate,” he said.
The outbreak of fighting on Sunday morning was the first since Friday when brief but heavy exchanges of fire left an estimated 150 soldiers dead on both sides, on the eve of the country’s fifth anniversary of independence.
There were no details of casualties from Sunday’s shooting.
The recent violence in the world’s youngest country represents yet another blow to a shaky peace deal that has so far failed to end the civil war that broke out in December 2013 when President Salva Kiir accused Machar of plotting a coup.