The sixth round of peace talks on Darfur were officially launched in mid-September but until Monday's meeting, government and rebel negotiators in Nigeria's capital had not held any direct discussions.
Instead, they attended several days of seminars on peace negotiating and then waited as Darfur's main rebel group argued about the makeup of its delegation.
The dispute between factions of the Sudan Liberation Army (SLA) is still unresolved, but African Union spokesman Assane Ba said talks on power-sharing had begun.
He said the factions agreed on an agenda to take talks forward, but gave no details.
Since the negotiating teams arrived in Abuja, officials say the situation in Darfur has become much worse.
Baba Gana Kingibe, the chief African Union envoy to Sudan, said on Saturday that Sudanese government forces attacked civilians in several areas of Darfur, committing acts of "calculated and wanton destruction" that have killed at least 44 people and displaced thousands more during the past two weeks.
"The information reported by Kingibe is incorrect, totally untrue and was obtained from the relief agencies, therefore Kingibe is considered a partial person and unworthy for this mission"
Al-Abbas Abd al-Rahman Khalifa, Sudan armed forces spokesman
He also blamed the SLA for launching attacks on two occasions.
AU chief mediator Salim Ahmed Salim said he could not understand "the killing of innocent civilians ... and the destruction of homes and the social fabric of communities in Darfur, when the major protagonists are all here in Abuja" to discuss peace.
The Sudanese government denied the African Union allegations on Monday.
"The information reported by Kingibe is incorrect, totally untrue and was obtained from the relief agencies, therefore Kingibe is considered a partial person and unworthy for this mission," said General al-Abbas Abd al-Rahman Khalifa, the Sudanese armed forces spokesman.
After decades of low-level clashes over land and water pitting nomads and villagers against one another in Darfur, rebels launched a large-scale conflict in early 2003, accusing the central government of neglect.
The central government is accused of responding by unleashing militias known as Janjawid to murder and rape civilians and destroy villages.
More than 180,000 people have died in Darfur and another two million people have been displaced in the fighting.