Egypt's interior ministry now says 20 Sudanese migrants have died after riot police broke up a makeshift protest camp in Cairo.
Thousands of police stormed the camp, set up near United Nations offices in September, wielding truncheons and firing water cannon at the protesters.
A stampede was reported as police forced hundreds of people onto buses.
In Geneva, the UN High Commissioner for Refugees, Antonio Guterres, said he was "deeply shocked" at the deaths.
"There is no justification for such violence and loss of life," he said.
The migrants had been demanding that the UN refugee agency (UNHCR) move them to a country with better conditions.
Thousands of police armed with sticks and shields stormed the small park where the migrants had been camping, at about 0500 (0300 GMT).
"There was a stampede that left 30 of the protesters injured, most of them the elderly and young and they were immediately taken to the hospital where 10 of them died," the interior ministry said.
Later the ministry raised the death toll to 20.
Journalists reported seeing a number of Sudanese people unconscious on the ground, some of them young children.
A girl aged about four was among the dead, doctors said.
Twenty-three police officers were wounded, the interior ministry said, accusing migrant leaders of inciting attacks against the police.
"Attempts have been made to convince them to disperse, but to no avail," the ministry said in a statement.
Witnesses said the migrants, including women and small children, were dragged towards buses as they tried to resist leaving the camp.
"They want to kill us," shouted one protester. "Our demands are legitimate, it is our right to protest here, the only right we have."
One of the Sudanese asylum-seekers, Napoleon Roberts, said he had been taken to a barracks south of the capital and was being held with about 1,700 others in disgusting conditions.
"We've been kept here since morning in disgust, and no water for drinking and no bathroom... people are staying still with their wounds on their bodies," he told the BBC's Focus on Africa programme.
Up to 3,000 protesters had been living at the camp since it was set up on 29 September, many of them sleeping in the open.
The demonstration began after the UNHCR stopped aid to those who had applied and failed to get refugee status.
A spokeswoman for the UNHCR in Cairo, Astrid Stort, told the BBC the agency had offered the migrants everything that was in its power.
"We have tried to convince them that some of their demands could be met but other demands were unrealistic," she said.
The UNHCR says it has to prioritise help for people genuinely at risk of persecution and cannot solve issues of discrimination and deprivation in Egypt, where unemployment is high.
It believes most of the demonstrators are economic migrants rather than those fleeing persecution, and so do not qualify as refugees.
But many of the protesters argue it is not safe to return to Sudan, despite a peace accord nearly a year ago which ended the 21-year north-south civil war.
A separate conflict in the western region of Darfur has displaced some two million people and left tens of thousands dead.