Buhari will visit South Africa next month to address the attacks and seek a solution.
Chairman of the Nigerians in Diaspora Commission, Hon Abike Dabiri-Erewa, while awaiting the arrival of the first batch of returnees also confirmed that there were immigration issues which caused the delay.
"I chose to leave because I value my life more than anything else because here is very hostile at the moment".More news: Massive Illinois train derailment sparks chemical fire, numerous evacuations
South Africa has faced widespread criticism for its latest outbreak of xenophobia or "Afrophobia" attacks as official responses included Nigeria boycotting the World Economic Forum Africa hosted in Cape Town last week, while Zambia and Madagascar also cancelled planned soccer games with South Africa's national team.
Precious Oluchi Mbabie, a 35-year-old Nigerian woman who has been working as a fashion designer and seamstress in a Johannesburg suburb, boarded the flight with her three children, leaving her husband behind.
Asked if he would return, the Nigerian said he has no plan to return to South Africa as what is happening may still happen in the future.More news: What we know so far about the nation's vaping illness outbreak
Moyo added that Harare would "escalate" the evacuation if the situation deteriorated.
South Africa does not know how many undocumented foreigners are in the country of 58 million people.
Retaliatory attacks in Nigeria forced South African businesses to shut doors for several days, and South Africa temporarily closed its embassy on safety fears. Democratic Republic of Congo, Bangladesh and Ethiopia topped the list of countries where people applied for asylum or refugee status in 2018.More news: Apple, Foxconn infringe China Labor Law at iPhone plant in Zhengzhou
It was not immediately clear how many people were on board the flight, operated by the private Nigerian airline Air Peace, but Nigeria's government said it estimated 313 people would board. He said his family was waiting for him in Nigeria.
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