Violence followed the prosecutor general's decision to charge ousted president Omar al Bashir over the killings of protesters during demonstrations that led to the end of his rule last month.
Sudanese security forces shot and killed six people, including an army officer, in overnight clashes with protesters behind the uprising that drove President Omar al Bashir from power last month, a medical union said Tuesday.
The violence came hours after protest leaders and the ruling generals reached a breakthrough agreement on transitional authorities to run the country.
The killings took place after nightfall on Monday, when protests in Sudan usually swell during the Muslim holy month of Ramadan that is marked by dawn-to-dusk fasting.
TRT World's Liz Maddock reports.
Just hours earlier, the prosecutor general's office said ousted president Bashir had been charged over the killings of protesters during anti-regime demonstrations that led to the end of his rule last month.
It was not immediately clear what punishment he might face.
Protest organisers say security forces killed around 100 demonstrators during the four months of rallies leading to Bashir's overthrow.
The official death toll is 65.
Three soldiers and several protesters and civilians were also wounded when "unidentified elements" fired shots at the Khartoum sit-in Monday night, the ruling military council said.
The Sudan Doctors Committee, which is part of the Sudanese Professionals Association that has been spearheading the protests said four 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.
Breakthrough in power talks
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, said.
"The authorities are as follows –– the sovereign council, the cabinet a d 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".
Talks to continue Tuesday
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.
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.
"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.
Following a deadlock in negotiations, the protest alliance on Saturday said the army generals had invited the movement for a new round of talks.
The generals in earlier talks had proposed the new council be led by the military, 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.
But the generals pointed to what they call "many reservations" over the alliance's roadmap.
They have singled out its silence on the constitutional position of Islamic sharia law, which was the guiding principle of all legislation under Bashir's rule.