Security forces stormed a protest camp in the Sudanese capital Khartoum on Monday and at least 13 people were reported killed in the worst violence since the overthrow of President Omar al-Bashir in April.
The military council took control of Sudan in April after ousting the long-ruling president, Omar al-Bashir, in a coup.
There have been reports of gunfire and explosions heard in the centre of Khartoum and neighbouring city Omdurman.
Demonstrators had closed off Street 60, one of the main streets in the capital with stone barricades and burning tree trunks and tires, an AFP journalist said.
While demonstrators have called for the TMC to step aside for a civilian government, the council claimed it tried to clear a limited area outside the sit-in and did not attack protesters inside.
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Reports indicate that during the military offensive carried out on Monday, 13 people were killed while 116 were wounded.
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.
By mid-day, security forces controlled nearly the entire camp, pushing out protesters and sealing off the area, two activists said. The Saudi and Emirati-backed Transitional Military Council (TMC), led by Lieutenant General Abdel Fattah al-Burhan refuses to give in to the protesters' demand to hand over power.
The African Union has called on the TMC and protest leaders to return "urgently" to negotiations, appeals which were echoed by Qatar and Germany.
Increasing numbers of troops in various uniforms - including the notorious desert camouflage of the Rapid Support Forces (RSF) paramilitary that have been blamed for other attacks on the protesters - arrived in pickup trucks throughout the night.
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The protesters and Sudan's military rulers had been negotiating over who should govern in a transitional period following the overthrow of Bashir after months of generally peaceful demonstrations, but the talks have become deadlocked. - General Abdel Fattah al-Burhan, interim leader of Sudan where security forces broke up a weeks-long sit-in in a deadly operation Monday, was largely unknown until seven weeks ago.
"The tents are there, and the youth are moving freely", he told Sky News Arabia.
The UN secretary general urged the Sudanese authorities to facilitate an independent investigation and to hold those responsible accountable.
"We, as Sudanese, hold the security forces accountable, based on eye witnesses, for the dispersal of the sit-in".
He also called "on the Transitional Military Council to protect the civilians from further harm", a statement said. "This. Must. Stop. Now", Ambassador Irfan Siddiq wrote on Twitter.
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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.