Thousands of south Sudanese poured out to vote for a second straight day in a landmark independence referendum on Monday, bringing the region a step closer to becoming the world's newest state.

Repeating the jubilant scenes witnessed on Sunday, huge queues formed outside polling stations in the regional capital Juba from long before dawn as voters seized the chance to have their say on whether to split Africa's largest nation and put the seal on five decades of north-south conflict.

The scale of the turnout on the first of the seven days of polling has already put the south well on the way to reaching the 60 percent threshold set by a 2005 peace deal between north and south for the referendum to be valid.

"The percentage of those who voted yesterday (Sunday) in the northern states was 14 and in the southern states it was 20 percent," Paulino Wanawilla Unango, of the South Sudan Referendum Commission, told reporters in Khartoum.

But a flare-up of violence in the disputed Abyei district on the north-south border, where the feuding Misseriya Arab and Ngok Dinka peoples both reported heavy losses over the past three days totalling at least 33 dead, overshadowed the massive referendum turnout.

Tensions in the district have been rising with the launch of the vote in the south. Abyei had been due to hold a simultaneous plebiscite on its own future which has been indefinitely postponed.

The three main Western brokers of the north-south peace process -- Britain, Norway and the United States -- expressed their "deep concerns" about the situation in the district on Sunday while also commending the "people of Abyei for their patience in recent months."

There was also deadly fighting in Unity state, a key oil-producing area near the north-south border where voting was suspended in some areas on Sunday after troops killed six militiamen over the previous two days, the southern army said.

In clashes in the state's Koch county on Monday, troops killed two loyalists of Gatluak Gai, the only south Sudanese militia leader still holding out against an amnesty offer from the authorities, military spokesman Philip Aguer said.

Provincial towns recorded similar crowds outside polling stations to those in the regional capital.

The governor of Western Bahr al-Ghazal, Rezik Zackaria Hassen, said: "We believe we can complete all the voting in four days."

In Lakes state farther east, governor Chol Tong Mayay said: "The only complaints were those who left disappointed after waiting so long in the sun but who did not get to vote because the time ran out.

"Many had to walk three or four hours each way to reach a centre but they can vote today or in the following days," he added.

In Juba, many voters took drastic action to ensure they got to vote on the second day after being disappointed on Sunday.

"I came at 2:00 am. Today I was the first to vote," James Khor Chol, 28, said proudly.

Like many in this mainly Christian region, Chol had gone to church on Sunday before going to the polling station where he was overwhelmed by the queues.

Many were wearing their Sunday best again on Monday as they cast their votes on whether to break away from the mainly Arab Muslim north.

A total of 3.93 million people are registered to vote in the referendum, some 3.75 million of them in the south.

Provisional results for the southern states will be not be announced until January 30, but polling stations will begin declaring their returns from Saturday, Wanawilla said.

Collating of the results takes so long because of the problems involved in collecting ballot boxes in a vast, war-ravaged region which has just 40 kilometres (25 miles) of tarmac road.

The independence referendum is the centrepiece of the 2005 north-south peace deal that ended a devastating 22-year civil war in which some two million people were killed and another four million fled their homes.

Sudan President Omar al-Bashir, an army man who led the north's war against the south for a decade and a half before signing the peace deal six years ago, has said he will respect the vote's outcome if it is "free and transparent."