Ghanaian nationals queued at Johannesburg's OR Tambo International Airport early on Wednesday to board one of the first flights home after waves of anti-immigrant protests in South Africa heightened safety concerns.

The group of 300 people included women and children, in what authorities described as a voluntary repatriation process for Ghanaian citizens who say they no longer feel safe.

South African authorities have been working with Ghanaian authorities on a list of around 800 people who have indicated they want to leave.

A South African immigration official, who was not identified on screen, told local television station eNCA: "What we found is that of the 300, only 10 of them are legal in the country, so quite a number of them are in non-compliance to our immigration act."

The repatriation followed a wave of anti-immigration protests in recent weeks, with campaigners demanding tighter controls on what they described as undocumented migrants, and accusing foreigners of contributing to crime and unemployment.

The protests have been accompanied by instances of violence against migrants from other sub-Saharan African countries.

One Ghanaian preparing to leave said repeated harassment had driven the decision.

"I'm happy that I'm going to my country ... it's not easy to be in someone else's country and be disturbed all the time," he said, declining to give his name.

Migrant rights groups say they are being scapegoated by South Africans who blame them for the country's economic problems, namely high unemployment which hovers at over 30% and disproportionately affects the Black population.

Ghana's High Commissioner to South Africa, Benjamin Quashie, said the departures were part of efforts to ease tensions while preserving strong diplomatic ties between the two countries.

"The demonstrators have said they want us to work together. We must ensure that those who are undocumented are returned home and that institutions are allowed to function," Quashie said, dismissing speculation of a diplomatic rift with South Africa.

South African authorities have condemned violence against foreign nationals and pledged to crack down on xenophobic attacks, saying such acts have no place in the country's constitutional democracy.