The National Chairman of the Christian Association of Nigeria in South Africa, Benson Uhwa, says there are Nigerians languishing in the country's police custody for violating visa rules.
Uhwa said arrangements were being made to repatriate them to Nigeria.
Air Peace is volunteering to fly home for free Nigerians interested in leaving South Africa.
However, there was an initial hitch as many of the would-be returnees had travel documents issues.
Uhwa, a member of the Nigerian community coordinating the evacuation of Nigerians over the ongoing xenophobic attacks in South Africa, also accused the South African government of refusing to deport foreigners.
There was a fresh xenophobic attack in Johannesburg on Sunday. One person was confirmed killed and five injured.