Ousted president Omar Al Bashir has been "charged with incitement and involvement in the killing of protesters" during anti-regime demonstrations that ended his rule last month.
Bashir is also facing an investigation over allegations of money laundering and terror financing.
On Monday, protest leaders and the ruling military council said they had agreed on a transitional power structure.
"At today's meeting, we agreed on the structure of the authorities and their powers," protest movement spokesman Taha Osman told reporters, adding that another meeting would be held on Tuesday "to discuss the period of transition".
This comes as violence flared in Sudan’s capital Khartoum, leaving five protesters and an army major dead.

US, Iran envoys head for talks, Israeli strikes continue after ceasefire
Israel and Hezbollah agree to ceasefire
Ebola cases in DR Congo rise to 933, with 245 deaths
Woman killed, 1,700 evacuated in beach hotel fire in Dominican Republic
One killed and several injured in train collision north of London, police say