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.
A Sudanese army major and a protester were shot dead Monday at a Khartoum sit-in, hours after protest leaders and the ruling generals reached a breakthrough agreement on transitional authorities to run the country.
The major was killed and three soldiers were wounded along with several protesters and civilians when "unidentified elements" fired shots at the Khartoum sit-in, the ruling military council said, as crowds of protesters remain camped outside the military complex.
A protester too was killed at the sit-in after he was shot in the chest, a doctors' committee linked to the protest movement said.
The umbrella protest movement the Alliance for Freedom and Change said the violence was to "disturb the breakthrough in the negotiations," blaming the bloodshed on the former regime.
Monday's violence erupted hours after the generals and the protest movement said a breakthrough had been reached in their talks over handing of power to a civilian administration.
"At today's meeting we agreed on the structure of the authorities and their powers," Taha Osman, a spokesman for the protest movement, told AFP.
"The authorities are as follows: the sovereign council, the cabinet and the legislative body.
"Tomorrow the talks will continue to discuss the period of transition and the composition of the authorities."
Sudan's army rulers and protest leaders resumed crucial talks on Monday over handing power to a civilian administration after a deadlock in negotiations.
The army generals and protesters are at loggerheads over who will sit on a new ruling body that would replace the existing military council.
The generals have proposed that the new council be military led, while the protest leaders want a majority civilian body.
Late last month, the alliance – which brings together protest organisers, opposition parties and rebel groups – handed the generals its proposals for a civilian-led transitional government.
TRT World's Khalil Charles has more details.
Sudan's ousted president Omar al Bashir has been charged over the killings of protesters during the anti-regime demonstrations that led to the end of his rule, the prosecutor general announced on Monday.
"Omar al Bashir and others have been charged for inciting and participating in the killing of demonstrators," the office of Sudan's acting prosecutor general Al Waleed Sayyed Ahmed said.
The charges against Bashir came during an investigation into the death of a medic who had been killed during a protest in the capital's eastern district of Burri.
"The prosecutor general has recommended speeding up of the investigation of the killing of demonstrators," the statement from his office said.