The attack on Malakal, one of the south's three main settlements, marked an escalation in a wave of clashes between the south's army and militias which has aroused fears over the stability of the region in the countdown to its secession, due on July 9.

"There is fighting going on in Malakal. Militia have penetrated the town. They raided at night," said southern army spokesman Philip Aguer on Saturday morning.

Aguer blamed the attack on fighters he said were aligned with renegade leader George Athor, a former army officer who rebelled last year saying he had been cheated out of the governorship of neighbouring Jonglei state in elections.

In January, southerners overwhelmingly voted to declare independence in a referendum promised in a 2005 peace deal that ended decades of civil war with the south.

The southern army and government has accused the north of backing militias in the south to destabilise the region and keep control of its oil, an allegation dismissed by Khartoum.

Aid workers in Malakal told Reuters they were woken at about 4 a.m. (0100 GMT) by the sound of gunfire and shelling.

"We're not that close to the fighting but the buildings here were shaking.

I was lying under my bed," said one humanitarian official, speaking on condition of anonymity.

A Malakal resident, who did not want to be identified, said he had seen the bodies of several civilians killed in the clashes.

The southern army said the fighting started in the centre of town.

Later, U.N. official David Gressly told Reuters the clashes were concentrated in the north of Malakal, near its airport.

Malakal is the administrative centre of Upper Nile, a volatile state bordering north Sudan and Ethiopia. It is the base for many U.N. agencies and international aid groups.

                                                   Copyright Reuters, 2011