The Eritreans had been arrested over the past two months and were flown back to their country's capital Asmara, the sources said.
Actvists have said that Eritrean immigrants face the risk of torture if they returned home. Many of them arriving in Egypt are Pentecostal Christians escaping religious persecution and others are trying to avoid military conscription, they said.
Many African migrants, some of whom are killed by Egyptian police as they scale the border fence with Israel, seek work in the Jewish state.
Last month Human Rights Watch said Eritrean migrants could face torture if forced to return home because the Asmara government regarded people who flee as having "betrayed" Eritrea.
The rights group said at the time Egypt was holding some 98 Eritrean migrants in a detention centre in Sinai and that the office of the U.N. High Commissioner for Refugees had not been granted access to them.
Egypt for years tolerated tens of thousands of Africans on its territory, but its attitude hardened in 2007 after it came under pressure to stop growing numbers of Africans trying to cross into Israel.
Egypt started a crackdown in June with deportations of hundreds of Eritrean asylum seekers, the largest in decades. Egyptian police shot dead at least 28 African migrants at the border with Israel in 2008.