Six people were killed in clashes between rebel militias and south Sudan's army, the military said, a day before a referendum in which the south is expected to vote for independence.
The attacks cast a shadow over celebrations in other parts of the south - attended by Hollywood star George Clooney and former US president Jimmy Carter - of the countdown to tomorrow's vote on whether the oil-producing region should secede.
The reports were a reminder of the deep rifts in the undeveloped south, which has been plagued by ethnic killings, rival militias and cattle rustling raids.
Philip Aguer, a spokesman for the southern Sudan People's Liberation Army (SPLA) said his forces ambushed fighters loyal to militia leader Galwak Gai in oil-producing Unity state yesterday and Gai's men launched a counter-attack today.
"They were coming from the north to disrupt the referendum. It is a known game. The spoilers are always here. They definitely came from Khartoum," he said, adding that SPLA forces killed two of Gai's men and captured 26 yesterday, then killed four today.
Gai was among several southern militia leaders who rebelled after April elections, accusing the south's government of fraud.
Southern leaders have regularly accused north Sudan of backing militias to try and disrupt the referendum in a bid to keep control of the region's oil. Northern leaders have dismissed the accusations.
Tomorrow’s referendum was promised in a 2005 peace accord that ended decades of north-south conflict - Africa's longest civil war that killed an estimated 2 million people. The fighting left deep rifts between southern communities and analysts have warned old tensions could re-emerge to destabilise the region.
The referendum's organising commission said it had everything in place to start processing around 4 million registered voters for the week-long voting exercise.
"Today we have nothing to do. We are waiting for tomorrow ... A couple of months ago, no one believed this would be possible," said Barnaba Mariel Benjamin, chair of the South Sudan Referendum Board (SSRB), in the south's capital Juba.
Preparations for the vote have been hit by logistical problems and delays. Northern and southern leaders also remain at loggerheads over how they would divide out oil revenues after a split and other issues.
Juba was festooned with pro-independence banners today as youth groups and campaigners held rallies and spontaneous celebrations in the count down to the vote.
Southern president Salva Kiir repeated promises that there would be no return to war with the north. "We are left only with a few hours to make the most ... important decision of our lifetime. I urge you to make the decision in a peaceful manner," he said in a speech in Juba.
Clooney, a long time campaigner in Sudan, particularly over its separate Darfur conflict, flew back to the capital after a quick visit to the contested central region of Abyei. "There is such an electricity in the air (in Juba)," he said. "I've never been around a place that gets to vote for their independence. To see the beginning of a new country, to see a country and a people that has longed for this for generations, to see the excitement that is in their eyes and in their hearts is really something spectacular to be around. It is an honour."
Reuters