In the post ― in which the prime minister refers to the African migrants as "infiltrators", a term Israeli public officials have commonly used for undocumented immigrants ― Netanyahu said he would meet with Interior Minister Aryeh Deri and representatives of the Israeli residents of southern Tel Aviv before reconsidering the deal.
Prime Minister Benjamin Netanyahu named Canada, Italy and Germany as some of the nations that will take in the migrants - although not all appeared to have been informed of the plan yet.
For each migrant resettled overseas, Israel will give "temporary residence" to a migrant in Israel, Mr Netanyahu told a news conference.
Where are the migrants from?
In February, Israel started handing out notices to 20,000 male African migrants giving them two months to leave the country or risk being thrown in jail.
Most of the African migrants in Israel, estimated at almost 42,000, are from Eritrea and Sudan. The border has since been strengthened, all but ending illegal crossings.
The decision triggered large protests in Israel and outrage among the Jewish community overseas - including former ambassadors and Holocaust survivors. The UN refugee agency said it could not immediately comment on the matter, but a spokeswoman said it would release a statement later in the day.
Canada is set to take in a number of African migrants from Israel, according to the United Nations refugee agency, but a late-in-the-day declaration from Israel's prime minister has put the fate of the deal in question.
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Rwanda, and possibly Uganda, were believed to have been the destination countries, according to reports, which also said the migrants' rights have been violated in the third country.
Opposition leaders and activists in Israel hailed the new deal on Monday.
But the agreement to let many of them stay in Israel drew harsh criticism from some of Mr. Netanyahu's right-wing coalition allies.
Michal Rozin, a member of Israel's parliament and a lead campaigner against the expulsions, said the agreement represented the "success of the Israelis who protested against the evil of deportation".
He called it a "total surrender to the false campaign in the media" and said the credibility of the government was at stake.
The U.N. refugee agency, the U.N. High Commissioner for Refugees, said a joint working group would come up with a plan for African migrants in Israel. According to the agreement, Israel will deport over 16,000 refugees and grant temporary residency status to 16,000 other refugees within a time frame of five years.
Only a handful of asylum claims have been approved in recent years.
Israel had announced a deal with the UNHCR to cancel a controversial plan to deport African migrants and replace it with one that would see thousands sent to Western countries.