Garrisoning the rebels, which would be a precursor to disarmament, was one item on the agenda which Nigerian President Olusegun Obasanjo had earlier said was unanimously adopted by all sides on Tuesday.
At the end of the morning session, Obasanjo announced to journalists: "I think we have made some progress. We've made the first step in the right direction in these very important talks."
However, the chief negotiator for the Justice and Equality Movement, Ahmad Muhammad Tugud, told reporters at talks in Abuja his group objected to a reference in the agenda to the cantonment of its forces.
"We have clear reservations on the agenda and this is important because we do believe agendas should be agreed upon," he said. "We need this issue - the issue of the cantonment - taken out of the agenda."
Rebel leader Abd Al-Wahid
Muhammad almost halted talks
Nevertheless, he confirmed that the rebel movement would return to the negotiating table at 9am on Wednesday for further discussions.
AU leaders hope that if agreement on a political and security strategy can be reached it will reinforce efforts to enforce a ceasefire in the western Sudanese region, where more than 30,000 people have died in the past 18 months.
The rebel groups, however, say they want the African Union to pressure Khartoum into granting Darfur and other regions greater autonomy and a better share of the national income.
They are also refusing to disarm.
"How can we disarm our people? Without a proper security arrangement, these forces are our guarantee," declared Abd Al-Wahid Muhammad Ahmad al-Nur, leader of the Sudan Liberation Movement (SLM), as he arrived at the talks on Tuesday.
The SLM and their allies the Justice and Equality Movement (JEM) are seeking amendments to the agenda to reinforce their demands for greater political and economic power for regions which they say are marginalised by Khartoum.
"The regions should elect their own government and hold it to account. The regions should have their own constitutions," JEM spokesman Ahmad Husayn Adam said. "We're not seeking to separate from our country, we want to be equal."
For their part, the Sudanese government accused the rebels of breaching an existing ceasefire agreement, including an attack at the weekend in which four Sudanese humanitarian workers and two journalists were allegedly kidnapped.
"We're not seeking to separate from our country, we want to be equal"
Ahmad Husayn Adam,
"Despite all that, we will continue to participate in these negotiations with the same spirit. Hopefully there will be an agreement between us and the rebel groups," the government party's spokesman Ibrahim Muhammad Ibrahim said.
There is no official date for the talks to end in Abuja - officials expect them to go on for several more days - but there is an implicit deadline in a looming United Nations Security Council ultimatum.
The UN has given Sudan until the end of the month to demonstrate that it is serious about restoring peace and security to Darfur, or face the prospect of sanctions.