Sudanese protesters wave national flags at the sit-in outside the military headquarters in Khartoum.
The number of people killed in the dispersal of a protest camp in the center of the Sudanese capital Khartoum on Monday rose to more than 30, an opposition-linked doctors' committee said.
The committee said the number was likely to rise as many casualties are still unaccounted for.
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.
But protest leaders said the site had been cleared of demonstrators.
"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.
It called on Sudanese to take part in "total civil disobedience" to topple the military council.
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 neighbourhood 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.
The military council "did not disperse the sit-in by force," its spokesman said.
"The tents are there, and the youth are moving freely," Shamseddine Kabbashi told Sky News Arabia.
Protests erupted in towns across Sudan in response to the violence in Khartoum.
"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 US 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 neighbouring 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 Military Council bears full responsibility for this action and the international community will hold it to account.
Stability in Sudan is crucial for a region grappling with violence that stretches from the Horn of Africa to Libya.
The TMC has repeatedly said it would not use force to disperse the protesters, often comprising thousands of young men and women who take turns camping outside the Defence Ministry.
No statement about the violence has yet been issued by the TMC.
The British Ambassador in Khartoum said in a message on his Twitter account he was "extremely concerned by the heavy gunfire I've been hearing over the last hour from my Residence and reports that Sudanese security forces are attacking the protest sit-in site resulting in casualties".
"No excuse for any such attack. This. Must. Stop. Now," he wrote.
Live footage broadcast by Arab television stations showed chaotic scenes, with protesters running away as black smoke rose from tents apparently torched by the raiding force.
A Reuters witness saw troops wielding batons deploy in central Khartoum and close roads, apparently to try to block people from reaching the protest site.
“Extremely concerned by the heavy gunfire I've been hearing over the last hour from my residence and reports that Sudanese security forces are attacking the protest sit-in site resulting in casualties.
Nile bridges that connect various parts of the Sudanese capital have also been blocked.
The sit-in had become the focal point of protests that started in December, sparked by a severe financial crisis that caused cash shortages and bread price hikes.
Sudan, one of the largest countries in Africa, has long been on a US list of countries that support terrorism, which has hampered foreign investments.
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 "Justice First" marches were called by the Sudanese Professionals' Association, which has been spearheading the protests since December.
Medics said on Monday more than 35 people were killed in what is the worst violence since the overthrow of President Omar Al Bashir in April.
Around 5,000 protesters marched peacefully from the Atash camp for the displaced to a military installation housing the 16th Infantry Division, SUNA said, citing South Darfur's governor. Sudan has seen frequent protests near military buildings.
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