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Tens of thousands of African migrants will be out of Israel in a plan that will be implemented on Wednesday, with those remaining under threat of arrest.

At the start of a cabinet meeting, Israeli Prime Minister Netanyahu said: "The plan will get under way today."

The plan will see the 38,000 African migrants, mainly Eritrean and Sudanese, who have entered the country illegally, leave by the end of March.

African migrants have been promised a plane ticket and $3,500, however those that miss the deadline and refuse to leave, will face arrest.

Holot, an open facility in the desert that can host 1,200 migrants who are allowed to leave to work during the day is also set to be closed.

The facility currently houses 970 people according to a statement released earlier this week by the interior ministry.

Previously, Public Security Minister Gilad Erdan said Holot had become "a hotel for infiltrators at the tax-payers' expense that does not encourage their exit" and costs 240 million shekels ($68 million, 58 million euros) a year.

The programme, originally approved in November has drawn the criticism of the United Nations refugee agency.

Wednesday's cabinet meeting formally moved the plan from the planning stage to action, said migrant aid worker Adi Drori-Avraham to AFP.

Nationalist anti-immigration protests regularly turn violent with random beatings of Africans and the ransacking of their properties or shops.

"We see here the implementation of the decision," said Drori-Avraham of the Tel Aviv-based Aid Organisation for Refugees and Asylum Seekers in Israel (ASSAF).

Africans in Israel only receive short term residence visas which need to be renewed every two months.  

"From today when a person goes to request an extension to their visa, if he does not have a pending asylum application, his visa will not be renewed, and he will be given a deportation order," Drori-Avraham added.

The new regulations mean that authorities are not required to "threaten them with a choice of voluntary departure or jail, simply to seize them and take them to a plane".

"At the moment there are exceptions for women, children, parents of children and victims of human trafficking, but the procedural rules make it clear that those exemptions are only temporary," she added.

A sharp shift to the right in Israeli politics has given rise to an increasingly vocal push to isolate African asylum seekers and ultimately return them to their homelands. Darfur and Eritrea, being the majority, are both riddled by instability, long running conflicts and political oppression.

Between January 2016 to March 2017, a total of 311 citizens of Sudan and Eritrea were detained without trial.

Nationalist anti-immigration protests regularly turn violent with random beatings of Africans and the ransacking of their properties or shops. 

Demonstrators have chanted slogans such as: "Stop talking, start expelling" and "Blacks out!", while other protesters have derided the "bleeding-heart leftists" working to help them.

Netanyahu has defended the plan, saying "every country must maintain its borders, and protecting the borders from illegal infiltration is both a right and a basic duty of a sovereign state".