The Department of Home Affairs says 268 Nigerian nationals left South Africa on Wednesday night through a voluntary process coordinated by South African and Nigerian authorities.
The group departed from OR Tambo International Airport after registering to return to Nigeria.
The department said the process is voluntary and is being carried out with the Nigerian consulate.
The departures come amid rising concern among foreign nationals following recent anti-illegal immigration demonstrations by civil group March and March.
More demonstrations are expected on 30 June.
Around 300 more expected
Home Affairs said more Nigerians who registered to leave are expected to depart next week.
The department’s head of immigration enforcement, Stephen van Neel, said officials had already cleared 568 people through Home Affairs and other systems.
“So, the remaining about 300 will stand over until next Monday. That is the plan from the Nigerian Embassy,” Van Neel said.
He said officials were continuing to process those who had asked to return.
The department said some people cited safety concerns, while others indicated they simply wanted to go home.
Several flights planned
At least 1 000 Nigerians have been confirmed for voluntary repatriation.
Authorities are preparing additional flights to help those who have registered to leave South Africa.
The DHA said around 500 people had already been processed, with at least four more flights scheduled.
Nigeria’s consul general in Johannesburg, Ambassador Ninikanwa Okey-Uche, said the flights form part of arrangements to help Nigerian nationals return home.
“What we’re doing is getting our people home. We have four or five flights planned. Tonight is the first one,” Okey-Uche said.
Fears follow demonstrations
The operation follows weeks of uncertainty for foreign nationals in South Africa.
Recent anti-illegal immigration protests have left some migrants fearing for their safety.
South African immigration officials said screening is continuing as both governments work to ensure the departures remain orderly and voluntary.
The process also comes as authorities prepare to maintain a strong presence around demonstrations linked to March and March.
Home Affairs has not said whether more foreign nationals from other countries have registered for similar voluntary departures.