"No one will dig old monkey bones to back up a theory that I was once a baboon. Sorry," said Zwelinzima Vavi, former general secretary of the powerful trade union group Cosatu, a faithful ally of the ruling African National Congress (ANC).
"I am no grandchild of any ape, monkey or baboon -- finish en klaar (Afrikaans for "that's it")," he said on his Twitter account, which is followed by more than 300,000 people.
Vavi recalled that when South Africa was under apartheid rule he was a target of racist remarks "I been also called a baboon all my life so did my father and his fathers."
Apartheid ended in 1994 after Nelson Mandela was elected as the country's first black president in a democratic South Africa.
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Vavi's comments came after last week's discovery of Homo naledi, described by scientists as a new distant ancestor of humans.
The discovery of the ancient relative generated a huge amount of international interest.
It "breathes new life into paranoia," said prominent British biologist Richard Dawkins on his Twitter account this week. "Whole point is we're all African apes."
Lee Berger, an American working at Johannesburg's University of the Witwatersrand and overseeing the Homo naledi dig, tried to keep his distance from the charged debate, though he did specifically clarify that man doesn't descend from baboons.
"For our scientists the search for human origins is one that celebrates all of humankind's common origins on the continent of Africa," he told AFP.
The body of Homo naledi resembles that of a modern man, but researchers say its orange-sized brain places it closer to Australopithecus, a group of extinct hominids that walked on two legs and lived around 2 million years ago.
Some 1,550 fossils were unearthed in the "Rising Star", a cave located in the "Cradle of Humankind", a site 50 kilometres northwest of Johannesburg that has proven over the years to be a rich source for palaeontologists.