Approximately 500 Nigerian nationals began the repatriation process at the Nigerian High Commission in Pretoria on Wednesday as part of a voluntary return programme supported by the Nigerian government.
The group was transported to OR Tambo International Airport on Wednesday night, where they were expected to board a repatriation flight back to Nigeria.
The initiative comes amid growing interest from Nigerian nationals seeking to return home, with more than 1,000 people having registered for repatriation so far.
The repatriation programme is being funded by the Nigerian government and follows a June 30 deadline set by anti-migrant groups operating in South Africa.
Officials have indicated that the process is voluntary and forms part of efforts to assist Nigerian citizens wishing to return to their home country.
The latest group is among hundreds expected to depart South Africa in the coming weeks as authorities continue to process applications from those who have expressed a desire to participate in the programme.
Meanwhile, Minister of International Relations and Cooperation Ronald Lamola acknowledged that recent tensions surrounding anti-illegal immigration campaigns have had an impact on South Africa's diplomatic relations with some African countries.
However, Lamola cautioned against the spread of misinformation, particularly following reports from Ghana alleging that two Nigerians had been killed and 15 Ghanaians hospitalised after being assaulted during a protest in South Africa.
The minister stressed that South Africa and Ghana share longstanding historical and diplomatic ties that should be preserved.
"South Africa and Ghana have enjoyed strong fraternal relations for generations, and we want those relations to continue because we are part of the same African continent," Lamola said.
He added that while concerns around illegal immigration must be addressed, discussions on the issue should be based on verified facts.
"The only issue we are clarifying is that, as we deal with this matter, it must be done factually and not through misinformation," he said.