Israel is to allow 498 Darfur refugees, who entered the country illegally from Egypt, to stay in the country although their legal status remains unclear.
Egypt agreed to help prevent refugees crossing into Israel
An inter-ministerial team was appointed on Sunday to assist the refugees.
Officials said those from other parts of Africa already in the country would be expelled, along with new arrivals.
The number of Africans entering Israel from Egypt has declined in recent months after Egypt agreed to accept refugees sent back across the border.
The recent agreement was signed between Israeli Prime Minister Ehud Olmert and Egyptian President Hosni Mubarak.
Egypt also agreed to help prevent refugees crossing into Israel.
Israel estimates that 2,800 people, most of them Africans, have reached the country illegally through its border with Egypt over the past few years.
According to the figures released by Israel's government on Sunday, 150 refugees have crossed into Israel since early September compared with 900 who arrived in July.
The UN estimates that at least 200,000 people have been killed and more than two million people have been displaced since fighting began in the Darfur region of Sudan in 2003.
Israel's Interior Minister Meir Sheetrit has said that Israel - founded after the Nazi atrocities against the Jews in WWII - could not ignore the issue.
Earlier this month Mr Sheetrit said: "Israel, with its history, must offer assistance. It can't stand by and shut its eyes. But a quota must be set."