But doctors said Wednesday that 40 bodies had been pulled from the Nile, sending the death toll soaring to at least 108.
The African Union said on Thursday it had suspended Sudan until a civilian government was formed, intensifying global pressure on the country's new military rulers to give up power. "The agenda of the invitation is only related to the talks over the political crisis in Sudan", the source reportedly said.
"An employer at the civil aviation authority was also shot dead by the RSF after he refused to break up a strike by civil aviation employees since Tuesday", it added.
Most shops were shuttered on what would usually have been a bustling Muslim Eid al-Fitr holiday, with minor protests erupting outside mosques after Eid prayers.
The Rapid Support Forces grew out of the Janjaweed militias used by the government to suppress the Darfur insurgency in the 2000s, a campaign that prompted charges of genocide against its perpetrators.
An official from the group told the BBC that they had witnessed and verified the bodies in hospitals and that the death toll now stood at 100.
The TMC has been in power since long-time ruler Omar al-Bashir was deposed and arrested in a peaceful military coup in April that followed months of anti-government protests.
The opposition had been in talks with an interim military council over a civilian-led transition to democracy, but the negotiations faltered and this week's crackdown marked a turning point in the power struggle.
The AFC further called for a "total civil disobedience", and appealed to the Sudanese to lay down their tools "in order to let the whole world know that the people of Sudan's sole concern is to remove the entire security committee of the former regime".
Sudan has been rocked since December when anger over rising bread prices and shortages turned into protests against Bashir that culminated in the military removing him after a three-decade rule where he became a pariah in Western eyes.
The bloodbath is part of a broader move by the Transitional Military Council (TMC) to forcefully close down the protests and sit-ins in Khartoum and throughout the country.
Jean-Baptiste Gallopin, a political analyst and expert on the role of armed forces in revolutions, said the crackdown could be a trigger for an attempt by dissatisfied elements within the military to move against the current leaders.
"We in the military council extend our hand for negotiations without shackles except the interests of the homeland", its head, Lieutenant General Abdel Fattah al-Burhan, said on state TV.
The opposition says 113 people were killed in the storming of the camp and a subsequent wider crackdown. The Military Junta confirmed the area used for the protests was open to demonstrators and they were not denied access to it.
"Many of those attacked this morning were sleeping when the Rapid Support Forces and other Sudanese security agencies began unleashing deadly violence", Sarah Jackson, Amnesty International's Deputy Regional Director for East Africa, the Horn and the Great Lakes, said.
"What is clear to us is that there was use of excessive force by the security forces on civilians", said Stephane Dujarric, a United Nations spokesman.
Saudi Arabia, a major backer of the military rulers, had earlier sought a resumption of "dialogue between the various parties of Sudan".
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