From Ethiopia, the African Union's Peace and Security Council posted on Twitter that Sudan's suspension will remain in effect until "the effective establishment" of a civilian-led transitional authority, "as the only way to allow the Sudan to exit from the current crisis".
The leaders of the protest movement, who want a civilian government to take over the running of the country, said they were stopping all contact with the military and called a general strike.
The crackdown began with a violent dispersal of the protest movement's main sit-in camp, outside the military headquarters in the capital, Khartoum, on Monday.
The Central Committee of Sudan Doctors said the death toll rose Wednesday from the military crackdown to 108 dead and more than 500 injured after two days.
The health ministry says 61 people died nationwide in the crackdown, 52 of them by "live ammunition" in Khartoum.
In the build-up to the raid, talks had ground to a halt between the Transitional Military Council and the main opposition alliance - the Declaration of Freedom and Change Forces (DFCF) - amid deep differences over who would lead a transition to democracy.
The deputy head of the military council defended the violent suppression, claiming that the protesters had been infiltrated by rogue elements and drug dealers.
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Negotiations between the military rulers and protest leaders broke down over disagreements on whether a planned transitional body would be headed by a civilian or a military figure.
Numerous reports from Khartoum said the paramilitary unit, the feared Rapid Support Forces (RSF), was roaming the city's almost deserted streets, targeting civilians.
Members of the Rapid Support Forces, who rights groups say have their origins in the Janjaweed militias of Darfur, were on the streets of Khartoum on Thursday in pick-up trucks mounted with machine guns and rocket launchers, witnesses said.
He also promised to launch an investigation into the killing of the protesters.
Patrick Kapuwa, the chairman of the Peace and Security Council, said "punitive measures" would also be imposed on those standing in the way of a peaceful transfer of power in Sudan.
Sudan has been in a state of unrest after President Omar al-Bashir was overthrown in April.
A spokesman for the protesters said they would instead continue their pro-democracy campaign to pressure the military to hand over power to a civilian authority.
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The attack caused an worldwide outcry, drawing strong criticism from the United Nations, European Union, African Union and other observers. In one of the most shocking moments, troops pulled 40 bodies of the victims from the Nile in Khartoum on Wednesday.
Last April, the U.S. Embassy in Khartoum evacuated its non-essential staff members and their families from the Sudanese capital.
Protesters had called for the Islamic festival of Eid al-Fitr, marked on Tuesday and Wednesday this week, to be celebrated in the streets, as a gesture of defiance against the military.
On Tuesday TMC leader General Abdel Fattah al-Burhan announced that negotiations with protesters were over, all previous agreements were cancelled, and elections would be held within nine months.
Ethiopian Prime Minister Abiy Ahmed has met both the warring military council and opposition a day after the British embassy ordered the evacuation of non-essential Brits.
African and Western governments have been strongly supportive of the protesters but Arab governments, led by Saudi Arabia, have backed the military rulers.
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