Home Affairs Minister Aaron Motsoaledi has told the SABC 179 Nigerians left South Africa on board a private plane on Wednesday.
On Monday, a private individual, who owns the airline Air Peace, offered to repatriate approximately 600 Nigerians amid a wave of attacks aimed at foreign nationals, reported News24.
This is after the country was rocked by violent flare-ups and looting, much of it in Gauteng, where foreign nationals appeared to have been targeted.
At least 12 lives were lost during the violence in the province.
During a briefing in Cape Town on Tuesday, Defence Minister Nosiviwe Mapisa-Nqakula said 10 of the 12 people who were killed were South African, News24 reported.
Motsoaledi said Wednesday's flight was delayed because of problems at check-in.
"The final figure of people who left on Wednesday was 179. When we were doing our exit controls we found that four were children. One person was arrested for having a fraudulent South African visa. We couldn't allow him to leave because he had fraudulently obtained a visa. So, we handed him over to the police. Only 179 ended up boarding that plane," Motsoaledi told the SABC.
News24 earlier reported another flight provided by Air Peace was meant to fly to Nigeria on Friday.