Former Sudan President Omar al-Bashir has been charged with corruption.
The charges are related to laws on "suspected illicit wealth and emergency orders", the public prosecutor's office said, without giving more details.
The military ousted the long-time president in April following months of protests against him.
A military spokesman said on Thursday mistakes had occurred as generals ordered an end to a sit-in demanding a return to civilian rule.
The crackdown on 3 June left at least 61 people dead, according to officials, or 118, according to doctors aligned with the pro-democracy protesters.
Talks between the protesters and the Transitional Military Council (TMC) broke down after the violence.
Protest leaders then called a campaign of civil disobedience, which they later called off to enable the resumption of talks.
After a meeting between Tibor Nagy, the US assistant secretary of state for Africa, and Lieutenant General Abdel Fattah al-Burhan, the military said it hoped the US could "play a positive role".
Mr Bashir was overthrown and arrested on 11 April after three decades of authoritarian rule. He has not been seen publicly since he was detained.
In May he was charged with incitement and involvement in the killing of protesters.