The death of seven Sudanese protesters and an army major undermined a potential breakthrough on the formation of transition authorities to run the country.
Five of the eight were shot dead on Monday in Khartoum when "unidentified elements" fired shots at the sit in outside the military headquarters, prompting fears that the military council could be up to some mischief.
The latest developments came as the prosecutor general's office said ousted president Omar al-Bashir had been charged over the killings of protesters during anti-regime demonstrations that led to the end of his rule last month.
The umbrella protest movement the Alliance for Freedom and Change said Monday's violence was to "disturb the breakthrough in the negotiations" with army generals as it blamed the bloodshed on the former regime's militias.
Earlier on Monday, the generals and the protest movement said they had agreed on a "structure of the authorities and their powers" that would transfer authority to a civilian administration.
"The authorities are as follows -- the sovereign council, the cabinet and the legislative body," Taha Osman, a spokesman for the protest movement said.
He added another meeting was planned for Tuesday "to discuss the period of transition and the composition of the authorities".
The military council confirmed the agreement and the agenda of the meeting later on Tuesday.
"We will continue to discuss the percentage of participation... and the transitional period," council spokesman Lieutenant General Shamseddine Kabbashi told reporters.
The generals insist the transitional period should be two years, while protesters want it to be four years.
The crucial talks between the two sides follow a deadlock in negotiations.
The apparent breakthrough came as Sudan's acting prosecutor general Al-Waleed Sayyed Ahmed said Bashir "and others have been charged for inciting and participating in the killing of demonstrators".
The charges form part of an investigation into the death of a medic killed during a protest in the capital's eastern district of Burri, his office said in a statement.
Ninety people were killed in protest-related violence after demonstrations initially erupted in December, the doctors' committee said last month.
The official death toll is 65.
Mass protests which drove Bashir from office on April 11 are still being held outside the army headquarters, vowing to force the military council to cede power.
Prior to Monday's talks, dozens of protesters blocked Nile Street, a major avenue in the city, for the second consecutive day, an AFP correspondent reported.
Pressing their demand for a handover to civilian rule, protesters also blocked a road leading to the capital's northern district of Bahari.
Three protesters were wounded by "live ammunition" when security personnel tried to dismantle blockades put by demonstrators in parts of the capital, the doctors' committee said.
"We reject using force against the civilians ... we are calling on the military council to take its responsibility in protecting the peaceful protesters," the Alliance for Freedom and Change said.
The generals in earlier talks had proposed the new council be led by the military, while the protest leaders want a majority civilian body.