A plane carrying 127 illegal immigrants took off for the South Sudan capital of Juba, in the first wave of expulsions of tens of thousands of Africans, the daily Maariv said on its website.
The first charter flight left Ben Gurion airport near Tel Aviv overnight Monday carrying 127 men, women and children and was to arrive in Juba some four hours later, Maariv said.
"They will be leaving here at midnight (2100 GMT Sunday)," Sabine Hadad, spokeswoman for the Population and Migration Authority told AFP earlier, saying the first plane was carrying South Sudanese who had agreed to be voluntarily repatriated.
Over the past week, Israel has been conducting mass raids to round up illegal immigrants, most of them Africans, with the aim of sending them home.
"So far, more than 500 people have volunteered to leave, and 300 people have been arrested," Hadad said of the operation which began at dawn on June 10.
The vast majority of them are from South Sudan.
Those who agreed to leave voluntarily have been promised a plane ticket and a grant of 1,000 euros ($1,250) per adult or $500 (396 euros) per child, officials say.
By early evening, Terminal 1 was a hive of activity with hundreds of people signing forms and receiving money before the late-night flight, an AFP correspondent at the scene said.
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Israeli Prime Minister Benjamin Netanyahu said another plane would be leaving "next week."
"Today, the government will begin the operation to repatriate illegal work infiltrators to their countries of origin," he told ministers at the weekly cabinet meeting. "We will do this in an orderly and dignified manner."
Harel Locker, director general of Netanyahu's office, said that over the weekend, only 38 immigrants had crossed the border into Israel, in what was "the lowest weekend figure in years."
"Our message that there is no work in Israel for infiltrators and that they will no longer be taken to Tel Aviv but put in detention for long periods, is getting through," he told public radio.
Israeli figures indicate there are some 60,000 Africans in the country illegally, most of whom live in run-down neighbourhoods of south Tel Aviv.
Only a tiny fraction of them are from South Sudan, with rights groups putting their number at some 700, although Israeli officials say the number is at least 1,500.
Until recently, the South Sudanese were shielded by an Israeli policy giving them protection as a group from deportation.
But on June 7, a Jerusalem court overturned that long-standing policy, ruling that they were no longer at risk in their homeland and clearing the way for their mass expulsion.
Rising tensions over the growing number of illegal immigrants exploded into violence last month when a protest in south Tel Aviv turned ugly, with demonstrators smashing African-run shops and property, chanting "Blacks out!"
Israel, which reportedly backed South Sudan through its 1983-2005 war with Khartoum, recognised the new nation and established full diplomatic relations with its government shortly after it declared independence in July last year.