"They were taken with vehicles that belong to the Janjawid militias to an unknown destination", The Central Committee of Sudan Doctors (CCSD) said in a statement on Facebook.
The death toll from the raid on Khartoum's pro-democracy camp has reached over 100.
Burhan had previously announced he was skipping any negotiations with protest groups and said he would organise elections within nine months.
"The Sudanese people are not open to this TMC (Transitional Military Council) that kills people and we need justice and accountability before talks about any political process", he told AFP.
The military in Sudan has offered to resume negotiations with protest leaders over the transition period, one day after he scrapped all agreements with an opposition alliance.
China, backed by Russian Federation, blocked a bid at the UN Security Council on Tuesday to condemn the killing of civilians in Sudan after the United States, Britain and Norway denounced a plan by Sudanese military rulers to hold elections within nine months.
Dagalo affirmed that the military council does not seek governance, adding that they want to restore the country's standing by enforcing the law.
"The situation is very hard".
"There's a shortage of medical staff, a shortage of blood", said the doctor, who asked not to be named.
He said: "They kicked us out from two hospitals that were giving aid to the injured and the victims of the gunshots".
"Among the wounded there are still people in a serious condition and I expect the number of deaths to rise". Security forces have been seen in online videos, patrolling Khartoum districts.
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.
On Wednesday, hundreds of residents of north Khartoum blocked off streets with rocks, and waited by them in silence, a witness told AFP.
In the distance gunfire could be heard.
The United Nations said late Wednesday it was relocating some of its staff away from Khartoum, while Britain warned its citizens against all but essential travel and made a decision to pull non-essential staff from its embassy. Minor protests erupted outside mosques after Eid prayers but there were no reports of significant clashes with security forces.
China, backed by Russian Federation, blocked a bid at the UN Security Council on Tuesday to condemn the killing of civilians in Sudan and issue a pressing call from world powers for an immediate halt to the violence, diplomats said.
Eight European countries - Belgium, Britain, France, Germany, Italy, Poland, The Netherlands and Sweden - instead issued their own joint statement criticising "the violent attacks in Sudan by Sudanese security services against civilians".
He did not urge a return to negotiations but criticized some in the movement for "unjustified escalation" - an apparent reference to strikes called by the Sudanese Professionals Association in previous weeks - and said he had expected the military to escalate as well.
There was no immediate reaction from the protest movement.
A prominent anti-government politician, Yasir Arman, was beaten and arrested by Sudanese security forces during the violence, the British Ambassador to Sudan, Irfan Siddiq tweeted on Wednesday.
"We call for an agreed transfer of power to a civilian-led government as demanded by the people of Sudan", the United States, Britain and Norway said.
Saudi Arabia, which has close ties to Sudan's military council, said on Wednesday it was watching developments with great concern and called for more dialog.
Yankees emerge as 'true favorites' for Dallas Keuchel
And the only reason the Braves are there is for the stellar performances of Mike Soroka and Max Fried, two very young pitchers. The countdown of Dallas Keuchel's free-agency saga is nearly complete as the southpaw is expected to sign shortly.