Various organisations have condemned Dr HH Schmitz's policy of racist segregation at his Ventersdorp surgery in the North West.
Yesterday Sowetan published a story detailing how Schmitz's patients, both black and white, have "separate" consulting rooms at his surgery.
Ventersdorp mayor Cecilia Phoyane said her municipality was fighting a losing battle against racist behaviour in this small farming area.
She said she had tried to speak to Schmitz and his colleague, Dr JA Coetzee, about the racist practice.
"We have had two memoranda delivered to the magistrate against their unconstitutional methods.
"We are trying hard as a municipality to ensure that people's rights, especially the poor, are not violated."
The Human Rights Commission said Schmitz's alleged policy of segregation was a violation of the Equality Act.
Chief executive officer Tseliso Thipanyane said: "We will instruct our North West office to verify this, and then take up the matter with the equality court.
"This is a straight violation of the Equality Act and the very basis of our constitution, which is the guarantee of human rights."
The South African Medical Association said it would instruct its legal service division to investigate the cases.
"A letter will also be sent to Dr Schmitz to answer for himself. An inquiry into the matter will be instituted if his response to these allegations is unsatisfactory," said spokesman Bertha Scheepers.
Voicing his concern, Solly Phetoe, spokesman for Cosatu in the North West, said: "The department of justice is not serving the interests of the poor, the majority of whom are black."