Juba is hosting talks between the government of new Prime Minister Abdalla Hamdok and representatives from two umbrella groups of rebels that fought forces of now ousted President Omar al-Bashir in Darfur, Blue Nile and South Kordofan states, Presstv Reported.
The talks were launched on Monday in the presence of heads of state from Ethiopia, Egypt, Rwanda, Uganda and South Sudan.
The first face-to-face meeting between the adversaries was to take place in the South Sudan capital on Wednesday.
But Amar Amoua, secretary general of the Sudan People's Liberation Movement North (SPLM-N), told journalists his group would not continue unless the government withdrew from the area of the fighting, in the Nuba Mountains.
"Our coming back to negotiate... is bound by government decisions to clear all these things," Amoua, who is representing three different rebel movements, told journalists.
He said that for the past 10 days government forces had continued to attack their territory despite an unofficial ceasefire.
A chief was killed in the Nuba Mountains and several businessmen had gone missing, he charged.
"The government should withdraw its forces and stop... occupying new areas, we will not allow that," he said.
Dhieu Mathok, a member of the South Sudan mediation team, told AFP they were investigating the SPLM-N's complaints.
"We are still investigating it whether there are really attacks in those areas or not, but this will not stop the peace process. Usually in a negotiation these things happen but we are here to resolve the problems."
Mohammed Hassan, a spokesman for the Sudan delegation, attributed the fighting to an attack by herders on local merchants.
"The government regrets and condemns in the strongest terms these unfortunate events that keep happening in the area and in other parts of the country," he said.
"We also regret that these events took place at a time when people are entering peace negotiations, and the country and the whole of the region is united for the cause of peace in Sudan."
The new peace initiative comes after Bashir was toppled by the military in April.
Hamdok has been tasked with leading Sudan back to civilian rule, but he has said he also wants to end Khartoum's conflicts with the rebels.
The years-long bloodshed has left hundreds of thousands of dead and forced millions to flee their homes.