Sami told Radio Capital that the agreement did not mention the countries where the 16,000 migrants should be resettled as the deals are "made directly by us with the countries that are available".
"The agreement with the United Nations to absorb the infiltrators is bad for Israel", he said.
Netanyahu is set to meet with Israeli residents of areas with large migrant populations.
The country said the migrants would be given up to $3,500 for leaving within the next 90 days.
"We continue to believe in the need for an accord advantageous for all that can benefit Israel, the global community and the people who need asylum, and we hope that Israel reconsiders its decision", said a UNHCR spokesperson.
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The presence of the primarily Sudanese and Eritrean migrants in Israel has become a key political issue.
Netanyahu said on Facebook that Rwanda had in the past few weeks folded to vast pressure and backed out of the deal it had made with Israel to accept expelled migrants, prompting him to seek the new arrangement with the UNHCR.
Naftali Bennett, the education minister and head of the far-right Jewish Home party was instrumental in Mr Netanyahu's retreat, which at first took the form of a mere suspension.
Hardliners in Netanyahu's coalition strongly criticized the deal for allowing thousands of Africans to remain after the prime minister announced it.
Yesterday, countries indicated by Netanyahu as an example of a possible destination for migrants - including Italy and Germany - denied giving their consent to the agreement between Israel and the United Nations refugee agency.
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At the start of a meeting with south Tel Aviv residents, Prime Minister Netanyahu declared: "I have listened intently to the many observations about the agreement". Netanyahu faced heavy criticism from nationalist allies, even within his own ruling Likud party.
The agreement was created to end the possibility of forced deportations of thousands of migrants to Rwanda under a controversial plan put forward by Netanyahu in January. Rwanda, along with Uganda, had repeatedly denied getting into an agreement with Israel-even though both said they would welcome migrants if they arrived.
On Tuesday, however, activists took to the streets of Tel Aviv once again holding signs saying "Stop the deportations!"
In January, Netanyahu announced a "mission" to expel all illegal African migrants from the country.
Netanyahu had earlier stated that an "unprecedented understanding" with the UNHCR had led to the agreement which would have also allowed for thousands of other African migrants to stay in the Jewish state.
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The Supreme Court froze the deportations in mid-March in response to a petition.