"There are 645 Sudanese who are going to go back to Sudan. They are leaving by boat on Thursday ... They may be illegal immigrants. Why should we send a refugee back? If they have broken the law of the host country," she said.
The Egyptian Foreign Ministry said in a statement that around 650 Sudanese, who were in the country illegally and not refugees, would be returned to Sudan.
The United Nations' refugee agency earlier said it had received assurances from Egypt that Sudanese asylum seekers would not be deported to Sudan.
U.N. High Commissioner for Refugees (UNHCR) spokeswoman Astrid van Genderen Stort said the Foreign Ministry had not informed the organization that there would be deportations.
"Our representative was at a meeting at 2 p.m. (1200 GMT) with the ministry of foreign affairs and nothing was mentioned," Stort said.
"In general a refugee has the same rights and obligations as every other citizen and people who have broken the law have the right to undergo due process," she told Reuters.
In Washington, Human Rights Watch called the Egyptian move "irresponsible" and said it planned to seek a meeting with the Egyptian ambassador and to write to President Hosni Mubarak.
"It's shocking, shocking on several levels," said Bill Frelick, Refugee Policy Director at Human Rights Watch in Washington, D.C. "It's very distressing."
In such a chaotic situation, "it's really quite irresponsible on the part of the Egyptian authorities to be returning people," he added.
Egyptian police used sticks and water cannons on Friday to move up to 3,500 refugees who had camped outside U.N. offices in an affluent Cairo district for months demanding to be resettled in the West. At least 27 people were killed in the violence.
Talks between the Sudanese and the office of the UNHCR to end the protest broke down on December 22, after many protesters rejected a deal signed by their leaders.
The agreement included reviewing the status of the protestors, giving asylum seeker status to those not yet registered with the agency, and inviting applications for "one off" financial aid. Stort said the offer was still open.
Officials at a church in central Cairo, where up to 2,000 of the Sudanese had been housed since the protest ended, said the refugees had been dispersed by security officials and that the UNHCR had given them grants to find accommodation.
"Today UNHCR was able to give out a grant which allowed people to rent houses," Father Claudio Lurati said.
The refugees say they face racism, unemployment and a lack of education and healthcare in Egypt since they fled violence in Sudan. The UNHCR says it cannot move all refugees to the West.
Sudan's north-south civil war lasted over two decades and made 4 million people homeless. A separate conflict in the Western Darfur region has produced a further 2 million refugees.
A peace agreement in January 2005 ended the north-south civil war but many say it is still not safe to return home.
The UNHCR says it has more than 20,000 Sudanese registered with the agency in Egypt. It puts the total number of Sudanese living in Egypt at two million to three million.