On Wednesday, Israel closed the Holot detention centre for migrants in the southern Negev desert as part of the deportation plan.
Since Netanyahu announced his deportation plan, some Holot inmates have been transferred to the nearby Saharonim prison.
Others who had submitted asylum requests before January 1 were released pending a decision, Haaretz newspaper reported.
Immigration authority spokeswoman Sabine Haddad said 300 had been freed after agreeing to leave the Jewish state.
Those released were barred from living or working in seven cities with high migrant populations, including Tel Aviv — where most are concentrated — Jerusalem and the Red Sea resort of Eilat, she said.
Holot, an open facility where inmates were free to leave during the day but had to return at night, was opened in 2013 with the aim of siphoning migrants away from the cities, the immigration authority says.
Israeli officials say that no one they classify as a refugee or asylum-seeker will be deported, though the process of granting asylum has been criticised as extremely slow and biased against claims.
Only a handful of asylum claims have been approved in recent years.
The migrants’ presence in Israel has become a political issue.
Religious and conservative politicians have portrayed the presence of Muslim and Christian Africans as a threat to Israel’s Jewish character.
Netanyahu has pledged to “return south Tel Aviv to the citizens of Israel”, adding that the Africans were “not refugees but illegal infiltrators”.
Those opposed to the plan include Holocaust survivors who say the country has a special duty to protect migrants.