They were seeking to resolve the differences between the the three parties that signed a Declaration of Principles (DoP) to end the Dafur conflict.
"The hope is that as they (the delegates) proceed and more and more confidence is built among the parties, things will go faster," the minister said.
He commended the chief mediator at the talks, Tanzanian Salim Ahmed Salim, and his colleagues for what he described as their "excellent job in trying to push things forward."
Adeniji urged the delegates of the three parties to narrow their differences and reduce the time spent on preliminary issues.
He conceded, "Any negotiation takes a lot of time and patience, particularly if it involves political, social and economic issues and conflicts."
The meeting Friday was attended by representatives of the Sudanese government, the Justice and Equality Movement (JEM) and the Sudan Liberation Movement (SLM) as well as a mediation team from Chad, Libyan and Nigerian facilitators and international partners, AU spokesman Nourredine Mezni told AFP.
"We are progressing slowly but surely. The direct talks between the parties in the conflict which we had this evening is good for confidence-building. The talks were frank and helpful," Mezni added.
The leader of the Khartoum delegation, Magzoub Al-Khalifa also said that the direct talks among the parties was "very useful. It will advance the progress of work in Abuja."
The AU-sponsored talks between Khartoum and Darfur's main rebel groups resumed in Abuja on June 10.
Some delegates are already complaining of weariness over the slow pace of progress.
The private discussion on the DoP was to preceed a plenary session at which substantive political and economic issues would be discussed.
Although the AU said that the plenary session, suspended since June 10 would reopen "not later than Sunday, June 26", some delegates believe that it may not resume until next week.