Early Monday morning, Sudanese security forces entered the site, killing two "peaceful" protestors, and injuring several others with "live bullets", an opposition union of doctors, the Central Committee of Sudan Doctors (CCSD), said on their Facebook account.
Video broadcast live on social media and Arab television stations showed tents on fire at a long-established protest site and unarmed civilians running under the sound of heavy gunfire.
It said the assault on protesters and other civilians "is wrong and must stop".
Many streets remained blocked off by demonstrators who had erected barricades made from stones, tree trunks and burning tyres, although the protesters had departed.
"We call for continued struggle with full civil disobedience until the fall of" the Transitional Military Council, the group's statement says.
On Thursday, representatives of the Military Council Governor in Sudan said that the army meant to take action against the camp of protesters in the centre of Khartoum.
The military council "did not disperse the sit-in by force", its spokesman said.
"Wounded people are lying on the ground and reception area as there are not enough beds", said Azza al-Kamel, a doctor at the Royal Care Hospital near the sprawling sit-in area outside the military headquarters in the capital, Khartoum.
The TMC had offered to let protesters form a government but insisted on maintaining overall authority during an interim period.
Number of injured in Dzerzhinsk blasts totals 89, say authorities
The deputy governor of the Nizhny Novgorod region, Dmitry Krasnov, told Russian state television that "two people are missing". Eighty-five people have been injured with 15 treated for shrapnel wounds after a factory blast in central Russian Federation .
The military council said it was still committed to a political settlement and was ready to resume negotiations with the pro-democracy movement, but the protest leaders said they were cancelling the talks because of Monday's violence.
"The protesters holding a sit-in in front of the army general command are facing a massacre in a treacherous attempt to break up our sit-in", said the Sudanese Professionals Association, which has been spearheading the protests against al-Bashir and the military rulers since late a year ago.
"What is clear to us is that there was use of excessive force by the security forces on civilians", United Nations spokesman Stephane Dujarric said. "No excuse for any such attack", he said on Twitter.
"The Military Council bears full responsibility for this action and the global community will hold it to account", Foreign Secretary Jeremy Hunt wrote on Twitter. "The TMC can not responsibly lead the people of Sudan", added the U.S. Embassy.
Internet users reported connection problems.
By mid-day, security forces controlled almost the entire camp, pushing out protesters and sealing off the nearly one square mile area, two protesters said.
One video showed policemen swarming around a protester sprawled on the pavement, beating him with sticks.
The RSF is commanded by General Mohamed Hamdan Dagalo, the military council's deputy head. They spread and morph into calls for Bashir to quit after three decades of iron-fisted rule.
The military's role in ousting Bashir has raised fears among many Sudanese that their country could follow a similar path to neighboring Egypt after its 2011 uprising.