Said Djinnit, the AU commissioner for peace and security, said the situation was dangerous, but he did not expect "incidents to spread across Sudan".
In June, an eastern Sudan rebel movement, the Eastern Front, attacked government positions around Tokar and claimed to have made significant advances against government troops.
Khartoum confirmed that there was military activity in the region but denied rebel claims that it had carried out an aerial bombing campaign against civilian targets.
Meanwhile, Djinnit reaffirmed that the AU expanded force for the troubled Darfur region of western Sudan was on track, adding that the entire expanded force should be deployed before the end of September.
The AU is poised to increase its troop numbers in Darfur to more than 6000 from about 2700.
Additional troops from Rwanda, which already has troops on the ground in Darfur and is one of the main contributors to the expanded deployment, will start leaving for Darfur on 15 July, Rwandan Foreign Minister Charles Murigande confirmed.
Djinnit played down security incidents involving AU troops already in Darfur, including one incident where AU troops were forcibly disarmed, although he did say the African Union "took strong exception" to such incidents.
"You cannot expect to make a peacekeeping operation without incidents," he said. "Some groups do not have a clear understanding of the role of peacekeepers."
"That is why we were strengthening the capacity of AMIS (AU Mission to Sudan). They are deploying with enhanced capacity, with armoured personnel carriers. We are strengthening their capacity to defend themselves."
Foreign ministers from AU member countries spent part of Saturday discussing peace and security issues on the continent. The situation in Darfur, Togo, Ivory Coast and Somalia were also considered, diplomats said.
Speaking to Aljazeera on Sunday, Libyan AU mediator Ali al-Traiki said the Sudanese government and the two major rebel movements in Darfur had reached an agreement to resolve the conflict.
He added that the three parties would sign the agreement on Sunday morning in Abuja.
But Sudan's Minister for Humanitarian Affairs Muhammad Yusif Abd Allah said that disagreements remained and that the Sudanese Liberation Movement had not agreed to sign.
"Uncovered topics remained on Saturday. The talks we had have narrowed the differences. Maybe an agreement could be reached during the day [Sunday]."