Under a deal reached with the UNHCR just hours before the Israeli premier's announcement, over 16,000 migrants and refugees would be sent to various Western countries, while much of those remaining in Israel would be granted official status.
Israeli Prime Minister Benjamin Netanyahu on Monday suspended a resettlement deal for African migrants faced with deportation, just hours after his office had announced the agreement with the UN refugee agency.
"I've decided to suspend implementation of this accord and to rethink the terms of the accord," Netanyahu wrote on his Facebook page, saying his move was in response to criticism of the deal.
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.
The new accord would at the same time allow thousands more of the mainly Sudanese and Eritrean migrants to remain in Israel at least temporarily.
The migrants have become a political issue, with religious and conservative politicians portraying the presence of Muslim and Christian Africans as a threat to Israel's Jewish character.
A group of residents of southern Tel Aviv, where many of the migrants have settled, immediately denounced the new plan in a statement, calling it "a shame for the state of Israel".
Netanyahu said he would meet on Tuesday with residents of southern Tel Aviv.
Several ministers also said they opposed the accord with the UNHCR, on which they had not been informed before the announcement by Netanyahu's office.
The deal announced by Netanyahu's office appeared to end the possibility that many would be forcibly deported.
Instead, it would see a minimum of 16,250 migrants resettled in Western nations including Canada, Germany and Italy.
"The agreement stipulates that for each migrant who leaves the country, we commit to give temporary residence status to another," Netanyahu himself said in a televised address.
Germany and Italy, however, said they were unaware of any such resettlement deal for African migrants from Israel.
Netanyahu in January announced the implementation of a programme to remove migrants who entered illegally, giving them a choice between leaving voluntarily or facing indefinite imprisonment with eventual forced expulsion.
According to interior ministry figures, there are currently some 42,000 African migrants in Israel, half of them children, women or men with families, who were not facing immediate deportation.
As the migrants could face danger or imprisonment if returned to their homelands, Israel offered to relocate them to an unnamed African country, which deportees and aid workers said was Rwanda or Uganda.
But Netanyahu said that he had to abandon the initial plan because the option of sending them to a third country "no longer exists".
Rwanda and Uganda have said they would not accept those deported against their will.
Migrants began entering Israel through what was then a porous Egyptian border in 2007. The border has since been strengthened, all but ending illegal crossings.