Netanyahu had announced Monday afternoon that Israel agreed to cancel the planned expulsion of the migrants in the deal, which called for sending about half of the 35,000 African migrants to Western nations and allowing the rest to remain in Israel.
He added: "We do not have a contract, any understanding, formal or informal, with Israel for them to dump their refugees here".
The fate of migrants who entered Israel illegally by trekking across a desert border with Egypt, has posed a moral dilemma for a state founded as a haven for Jews from persecution and a national home.
At a news conference in Jerusalem, Netanyahu praised the new agreement reached with the UN Refugee Agency (UNHCR).
"In the past 24 hours, I have held many consultations with Interior Minister Aryeh Deri, with professionals and representatives of residents of southern Tel Aviv", Netanyahu said Tuesday in his announcement.
Under the deal between Israel and UNHCR, 16,250 African migrants under threat of being either jailed or deported to another African country, would instead be absorbed and resettled into a Western country.
A Palestinian was shot dead by Israeli forces on the Gaza border Tuesday, the health ministry in the strip said, as tensions remained days after 17 people were killed when a mass demonstration led to clashes.
"Occasionally a decision is reached that has to be reconsidered", he said Tuesday at a meeting with anti-migrant activists from south Tel Aviv, where numerous migrants reside.
In a joint statement, Israeli human rights groups condemned the decision to cancel the agreement, accusing Netanyahu of playing "political games".
SpaceX launches rocket with satellites from Vandenberg AFB
But this was one of the rare occasions Musk has acknowledged his rocket startup's attempts to recover the fairing after launch. Steven" to attempt to catch one of the payload fairing halves as they fell toward the Pacific Ocean.
Netanyahu said he had listened "attentively many comments on the agreement, and (.) after reassessing its advantages and disadvantages I chose to cancel it".
"I hear you, and first and foremost the residents of south Tel Aviv".
The deal put Netanyahu under fire from several conservative politicians, including some in his own Likud party.
As a result, thirty thousand Sudanese and Eritrean asylum seekers in Israel were hurled into limbo once again.
A group of residents of southern Tel Aviv, where numerous migrants have settled, immediately denounced the new plan in a statement, calling it "a shame for the state of Israel". But just hours later he reversed course, saying he was putting it on hold.
Israel's use of live fire has come under criticism from rights groups, while the European Union and United Nations chief Antonio Guterres have called for an independent investigation.
Israel has canceled a deal reached with the United Nations that would have relocated thousands of African migrants to the West, just a day after announcing the plan.
Hardliners in Netanyahu's coalition criticized the deal and pressured Netanyahu to suspend it.