A visiting delegation from South Sudan did not oppose the repatriation. Israel is offering a monetary incentive to migrants to leave voluntarily.
Some 60,000 impoverished Africans, most from Eritrea and Sudan, have slipped into Israel across its southern border with Egypt since 2005, fleeing repressive regimes and seeking work.
The influx has caused friction with Israeli locals, and several incidents recently turned violent.
Authorities, alarmed by the swelling numbers, say the migrants are a burden
Facing a public uproar, the government launched a campaign last week to round up and expel migrants from South Sudan and other countries that have friendly relations with Israel, and therefore would be expected to treat returning citizens well.
In all, it hopes to expel 4,500 Africans.
The operation would only make a small dent in the total number of migrants. Under an international treaty, Israel cannot deport those from Sudan, an enemy state, or to Eritrea, a country with a miserable human rights record, because they could face harm if they return to their homelands.
In addition, other Africans continue to flood into Israel. Interior Ministry spokeswoman Sabine Haddad said that while Israeli authorities rounded up about 300 people over the past week, some 260 more Africans entered Israel illegally.
Haddad said the people leaving Sunday had agreed to go after being threatened with arrest. In all, more than 500 agreed to leave within the past week, and another flight is scheduled for next week, she said. Adults who sign the voluntary departure form will receive 1,000 euros ($1,300) apiece to help them resettle, and minors will be given 500 euros ($650) each, she said.
South Sudanese Interior minister Alison Manani Magaya said a delegation of South Sudanese officials was in Israel to assess how many will return. She said those that did would be provided the same assistance given to Southerners returning from Sudan.
"They can come and stay with their relatives," she said. "They were there (in Israel) because of the (Sudanese civil) war. The war is over and they should come back home."
She insisted that South Sudan has no objection to Israel's move.
"That is their country. If they don't want people there, then they can come home," she said.
Many of the migrants have concentrated in impoverished neighborhoods, and their growing presence has created mounting tensions with locals who accuse them of rapes and other crimes. In an alarming recent development, several migrants and African homes and businesses have been attacked.
Migrants' advocates were appalled by the forced departures.
"They (the migrants) tell the cameras, we are happy, we are proud, but in private conversations, they tell us they're very afraid," said Orit Marom of the Asaf organization.
To Marom's criticisms, Haddad replied that the cash the migrants would receive "is equal to more than a year's salary" in South Sudan.
Prime Minister Benjamin Netanyahu, who has called the migrants "a national scourge," told his Cabinet on Sunday that the government has stopped allowing migrants to enter Israeli cities. Instead, they are to be arrested at the border and put into detention.
"Jews have a tradition of treating foreigners humanely, and even when we have to remove them from within our midst out of a state's desire to rule its borders, we shall do it humanely and express ourselves with restraint and humanity," he said.
Sigal Rozen, of the Hotline for Migrant Workers, an advocacy group that assists the Africans, warned of a potential backlash when the public realizes that the expulsion applies to just a small number of people. She estimated there are just several hundred South Sudanese in the country.
"The prime minister is exploiting the South Sudanese to give the impression that this is the beginning of a mass expulsion," she said.
A detention center the government had approved more than a year ago to hold thousands of migrants has not been completed, though Israel is working to build a fence along the Egyptian border meant to keep out both migrants and militants. In addition to the detention center, it plans to build a tent city to hold 20,000 other migrants.
Michael Onyiego contributed to this report from Juba, South Sudan.