Clashes between south Sudan's Army and rebel militiamen killed at least 55 people, a government official said on Sunday in the soon to be independent state gripped by a bloody wave of unrest.

The fighting raged for about three hours on Saturday in Jonglei state between the Southern Sudan People's Liberation Army (SPLA) and gunmen led by former militia leader Gabriel Tang, also known as Tang-Ginye.

"The shooting started in a place called Kaldak on Saturday morning, and there was heavy fighting," said Peter Lam Both, information minister for Upper Nile state, speaking from the state capital Malakal.

"Around 50 soldiers from Tang-Ginye, and five of his generals were killed."

There were no details of any deaths from the SPLA, but Both said dozens of wounded troops had been brought to Malakal for treatment.

"In the hospital here we have 34 SPLA soldiers wounded and 43 civilians," Both told AFP.

South Sudan is reeling from a series of violent rebellions that have already soured the mood ahead of full international recognition in July, with at least seven separate militia groups battling the Southern government.

In a separate incident in troubled Jonglei state, the UN's World Food Programme said a Sudanese staff member had been killed in an ambush on Friday in the Duk Payuel area, South of Kaldak, when gunmen attacked his vehicle.

More than 800 people have been killed and 94,000 people forced from their homes in fighting since January, according to UN estimates, when Southerners voted overwhelmingly for their own nation in a largely peaceful referendum.

Tang commanded a pro-Khartoum militia during the devastating 1983-2005 civil war between the North and the South, but agreed to join the Southern Army late in 2010.

His troops were due to be formally integrated into the SPLA under an agreement reached last week, with Tang taking the post of Lieutenant-General, Both said.

However, his fighters reportedly refused to follow orders to travel to the Southern capital Juba, sparking on Saturday's battle.

"Tang-Ginye's forces have scattered into the bush, and there are no reports of fighting so far today," Both said.

"We don't have exact information about Tang-Ginye himself, but he is believed to be with his forces," he added.

Tang's forces were involved in fighting inside Malakal in February, when they fought northern colleagues in a bid to retain heavy weaponry being transferred to the North.

Elsewhere, thousands of civilians are reported to have fled separate clashes in oil-producing Unity state, which neighbours Jonglei and Upper Nile.

No reliable death toll was available from the fighting in Unity state, with the rebels and the Army each claiming to have killed "several" on the other side, and dismissing each other's reports as lies.

The violence there has also forced the evacuation of 130 Northern oil industry workers back to the North.

Fighting in the South is raising concern for the plight of civilians, as the region gears up for independence.

Human Rights Watch last week accused both the Army and another rebel group of human rights violations against civilians during clashes in Upper Nile state in early March.