The death toll has risen to 27 Sudanese deaths from an Egyptian police operation to break up a protest camp.
The Sudanese migrants were forced onto buses
Thousands of police wielding truncheons and firing water cannon at protesters stormed the Cairo camp last Friday.
The migrants had been camped outside UN offices since September, demanding the UN refugee agency move them to a third country with better conditions.
There have been calls for the Egyptian authorities to launch an independent inquiry into the deaths.
Morgue officials said there were now 27 bodies, including 11 children.
A Sudanese newspaer says that flights will begin to Khartoum shortly on board Egyptian planes deporting the sit-in protesters.
Cairo's Notre Dame church is housing more than half of some 3,500 Sudanese protestors who Egyptian police forcibly moved from their camp.
The UN has said there is no justification for the violence and loss of life.
The Egyptian interior ministry blamed the deaths on a stampede. It also accused migrant leaders of inciting attacks against the police.
The government has ruled out an international investigation. Egyptian Foreign Minister Ahmed Aboul Gheit was quoted by the state news agency as saying: "Egypt has dealt with the sit-in of the refugees with wisdom and patience."
Refugees say hundreds are still being detained.
Several million Sudanese have been made homeless by conflict in the past two decades, but following a peace deal last year the UNHCR has now begun a voluntary repatriation programme.