Prosecutors have charged ousted President Omar al-Bashir with involvement in killing protesters and incitement to kill protesters during the uprising that drove him from power.
Sudan's state news agency published the charges, following a statement from the public prosecutor. It was not immediately clear what punishment Mr Bashir might face.
The transitional military council ruling Sudan has said he would face justice inside the country and will not be extradited to the Hague, where the International Criminal Court has charged him with war crimes and genocide linked to the Darfur conflict in the 2000s.
Mr Bashir, who was the only sitting head of state to be subject to an international arrest warrant, was imprisoned in the capital, Khartoum, days after the military removed him from power last month.
Demonstrators have nonetheless remained in the streets, demanding the dismantling of his regime and a swift transition to civilian rule.
They have threatened a general strike and civil disobedience, although negotiations continue with army leaders.
Lieutenant General Shams al-Deen al-Kabashi, a spokesman for the military council, said Monday's meeting, the first in over a week, was held "in a more optimistic atmosphere."
The protesters are represented by the Forces for the Declaration of Freedom and Change, a coalition of opposition groups led by the Sudanese Professionals Association , which has spearheaded the protests since December.
Lt Gen Al-Kabashi said they agreed on the creation of a sovereign council, a cabinet and a legislative body that would govern the country during the transition. He said they will discuss the makeup of the three bodies and the duration of the transition.
The two sides remain divided over what role the military, which is dominated by Mr Bashir's appointees, should have in the transition period until elections can be held.
The military wants to play a leading role in a transition lasting up to two years, while the protesters have demanded an immediate transition to a civilian-led authority that would govern for four years.
They fear the army will cling to power or select one of its own to succeed Mr Bashir. They also worry that Islamists and other factions close to the deposed leader, who is now jailed in Khartoum, will be granted a role in the transition.
The military agreed last month to recognise the FDFC as the uprising's only legitimate representative in a victory for the protesters. But the generals have called for other political parties — with the exception of Mr Bashir's National Congress Party — to be included in the transition.
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