Heavily armed security forces in pick-up trucks mounted with machine guns were deployed in large numbers all around the capital, while gunshots were heard from the protest site by an AFP journalist.
The United States and Britain called for an end to the crackdown on demonstrators, who want the generals behind the overthrow of veteran president Omar al-Bashir to hand over to civilian rule.
The Central Committee of Sudanese Doctors, which is close to the protesters, updated the death toll "raising the number of martyrs to 13" in a Facebook statement.
It also reported a "large number of critical casualties" and called for "urgent support" from the International Committee of the Red Cross and other humanitarian organisations to help the wounded.
The military council has denied multiple reports of their forces violently dispersing the sit-in in front of army headquarters, as protesters took to the streets in towns around the country.
"The Rapid Support Forces and the army and police and militia battalions dispersed the peaceful sit-in," the Alliance for Freedom and Change, the protesters' umbrella group, said in a statement.
Outside the army headquarters "there is no one, but the pure bodies of our martyrs that it has not been possible to evacuate from the site."
The Sudanese Professionals Association (SPA), which spearheaded nationwide protests that started in December, said it amounted to a "bloody massacre" and hundreds of people had been wounded.
The doctors' committee said forces were also opening fire inside the city's East Nile Hospital and "chasing peaceful protesters".
It said another hospital near the site of the sit-in was surrounded and volunteers were prevented from reaching it.
Rallies against Bashir's authoritarian, three-decade rule led to his ouster in April, but protesters had remained outside the army headquarters calling on the generals to cede power to a transitional authority.
Near the demonstration site, a witness living in the Burri neighborhood said he could "hear the sound of gunfire and I see a plume of smoke rising from the area of the sit-in."
Another resident of the area, in east Khartoum, said he had seen forces in "police uniform" trying to expel the demonstrators.
"Now the streets are closed (with barricades made) from stone and the chant is going round 'Just fall, that's all, the whole Council'," a witness in Port Sudan on the Red Sea said.
A witness in Atbara, in northern Sudan, said the city's roads were closed and "even the streets that link it to other towns."
Britain's ambassador to Khartoum, Irfan Siddiq, said he had heard "heavy gunfire" from his residence.
The country's foreign minister condemned "the attack on protesters by Sudanese security forces" and called it "an outrageous step."
"The Military Council bears full responsibility for this action and the international community will hold it to account," Foreign Secretary Jeremy Hunt wrote on Twitter.
The U.S. embassy in Khartoum said "security forces' attacks against protesters and other civilians is wrong and must stop."
"Responsibility falls on the TMC. The TMC cannot responsibly lead the people of Sudan," it added referring to the transitional military council.
The Alliance for Freedom and Change announced "the end of all political contact and negotiations with the putschist Council" following the deaths, even as neighboring Egypt appealed for the two sides to talk.
Negotiations between protest leaders and the ruling military council have broken down, as the two sides have failed to agree on whether a planned transitional body would be headed by a civilian or a military figure.
The rally leaders urged "peaceful marches and rallies" nationwide and for barricades to be put up including in the capital.
Protesters had already set about building a brick barricade and had set tyres and tree trunks alight on one of the main streets in the capital.
The army mustn’t get away with this. The Soudanese people deserve their freedom. Only in banana republics do armymen or clergymen rule. Saudi Arabia should drop this one and focus on their Puppets Sisi and Haftar which is plenty already,
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Sadly Saudi like Iran rules through the control of religion as a tool. Europe had its version of Arab spring back in 1914 and was not truly concluded till the Russians gave up their rule over the eastern European nations that have now split up to cover their ethnicity. The Arab world is going through that now, however if it took Europe over 70 years to get rid of its Ceaușescu's and house of Hapsburgs what will it take for the Arab world to do so?
Indeed, it took them as long to get rid of communism as well. Democracy has today shown its limits in the western world.. whilst Arabs are even still stuck at the previous stage. We need a new nahda/renaissance but it won’t happen anytime soon. Pollution, drought and other effects of global warming will however deal with the problem (us) before we revolutionize our societies. I’m very pessimistic as you can see.
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