As many as 42,000 African migrants have been ordered to leave the country within 90 days or face imprisonment. Israel has not clearly said where the immigrants will go but tacitly recognizes that it is too unsafe to return the Sudanese and Eritreans to their homes.
The country's authorities have threatened to be arresting every migrant if their commands on them are not met.
The government plans to close the Holot detention centre within three months, according to a statement issued on Monday by Israel's Population and Immigration Authority.
Netanyahu said a barrier Israel completed in 2013 along its border with Egypt had effectively cut off a stream of "illegal infiltrators" from Africa after some 60,000 crossed the desert frontier. Numerous illegal immigrants say they fled violence and persecution, but Israel treats them as economic migrants.
The United Nations refugee agency said the PIA's notice violates global and Israeli laws.
"We will return south Tel Aviv to the citizens of Israel, they are not refugees, but infiltrators looking for work", he said in August.
The elderly, children, and victims of slavery and human trafficking are reportedly exempt from the order.
Israeli Prime Minister Benjamin Netanyahu has characterized the resettlement of African migrants in Israel as harmful to the country's Jewish character and social cohesion. The ultimatum is part of a large-scale campaign to remove 42,000 illegal African migrants from Israel.
The Israeli government is considering giving each migrant a reported sum equivalent to $3,500 to leave, with the option of going home or to a third country. "We don't know what is waiting for us (in Rwanda and Uganda)", he told Reuters by telephone.
"We have no partnership agreement with the government of Israel, ask them (Israel) to explain how they reached that decision", the minister said.
The Hotline for Migrant Workers, an advocacy group, condemned the move, saying expulsions "put the refugees' lives in danger". The government now considers most of the "infiltrators" to be economic migrants.
Since 2009 when Israel took over the process from the UNHCR to determine who is a refugee, only eight Eritreans and two Sudanese have been granted this status.