The fighting hit a UN camp for displaced people sheltering from the violence, according to witnesses.
"The condition is really very bad. We have a lot of casualties this side, I think around 50 to 60 besides those of yesterday," said Budbud Chol who oversees security at a clinic in the base. "We have civilian casualties. We have rocket-propelled grenades that have landed in the camp which has wounded eight people."
At least one person has died in the camp, he said, but he did not know about casualties outside where the fighting is heavy.
Government forces attacked a rebel base in the Jebel area of the capital this morning, said William Gatjiath Deng, a spokesman for the rebel forces.
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"Three helicopter gunships have just come now and bombed our side," he said.
South Sudan's army confirmed the clashes today but it is not clear how the fighting started, said army spokesman Lul Ruai Koang, who is in the SPLA general headquarters at Bilpham.
There have been huge explosions in Gudele and people are fleeing by foot, said a resident, who spoke on condition of anonymity for fear for her safety.
"I've gotten calls that I should leave but there was so much gunfire nearby I decided to stay in," she said.
United Nations security radio reported fighting near the house of army chief of staff Paul Malong.
The UN Mission in South Sudan is on a high security alert with no movement of UN personnel whatsoever, said Shantal Persaud, spokeswoman for the UN mission.
Today's fighting is a resumption of the conflict on Friday in which more than 100 people died. A precarious calm was restored yesterday - the day South Sudan was to celebrate its fifth independence day - that was shattered by heavy gunfire today.