A Darfuri tribe says 55 of its members have been killed in a clash with soldiers from Southern Sudan's army.
A Rezeigat tribal spokesmen said the tribe had been looking for new pastures for its cattle when fighting erupted on Friday near the south Sudan boundary.
Southern Sudan accused the northern government of attacking and reported a new assault on Sunday, saying its troops had been forced to retreat.
It is the worst violence reported since Sudan's historic polls on 11-15 April.
The delayed results of the presidential elections being held in both Sudan and Southern Sudan are now due to be announced on Monday, the country's national elections commission has said.
The first multi-party polls in 24 years - a key part of the peace process for the divided country - were marred by irregularities and alleged fraud.
Those results that have been announced, mainly from the north, suggest President Omar al-Bashir's party has a strong lead.
He is widely expected to be re-elected while the Sudan People's Liberation Movement (SPLM) are likely to hold on to power in semi-autonomous Southern Sudan.
Friday's clash is certain to raise tensions, particularly in the sensitive border area, the BBC's James Copnall reports from Khartoum.
Mohammed Issa Aliou, a leader of the Rezeigat tribe of Arab nomads, said tribesmen had been seeking new pastures near the border with Southern Sudan's Western Bahr al-Ghazal province.
There are often clashes about grazing rights and water points in this area, our correspondent says.
At least 85 tribesmen were wounded, Mr Aliou said, adding that the tribe was sending reinforcements to the scene.
Speaking to Reuters news agency by telephone from southern Darfur, he said: "There was movement from the Rizeigat and from the SPLA.
"I can't tell you who attacked who first but they clashed."
SPLA spokesman Malaak Ayuen said late on Saturday that a company of Southern soldiers (about 120 men) had come under attack from northern government (SAF) forces.
"The SAF was using four land cruisers with mounted machine guns," he told Reuters.
Another SPLM spokesman, Maj Gen Kuol Deim Kuol, said the southern company had been attacked by "armed men wearing uniforms of the northern army".
Mr Ayuen later reported a new attack on south Sudanese forces in the same area. "They reinforced themselves and launched another attack and occupied the place," he said.
A northern armed forces spokesman told the BBC his men had not been involved in any fighting.