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 major and a protester were killed at a sit-in outside the army headquarters in Khartoum where thousands of protesters remain camped for weeks, demanding that the army generals who took power after ousting Bashir step down.
Three soldiers and several protesters and civilians were also wounded when "unidentified elements" fired shots at the Khartoum sit-in, the ruling military council said.
A doctors' committee linked to the protest movement later said four more protesters had been shot dead, but did not specify if they were actually killed at the sit-in.
The military council said in a late night press conference that it had "noticed some armed infiltrators among the protesters".
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 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," he said.
Osman said another meeting would be held on Tuesday "to discuss the period of transition and the composition of the authorities".
The military council confirmed an accord had been reached.
"We agreed on forming the transitional authority on all three levels -- the sovereign, the executive and the legislative," council spokesman Lieutenant General Shamseddine Kabbashi told reporters.
"Tomorrow we will continue to discuss the percentage of participation... and the transitional period."
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.
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