The commission says it has received numerous complaints about the comments Mngxitama made at a rally in Potchefstroom, where he told supporters "to kill white people and their pets".
In a video, Mgxitama says: "We will kill their women, we will kill their children, we will kill their dogs, we will kill their cats, we kill anything that comes for us."
"The South African Human Rights Commission has resolved to institute litigation on the matter at the Equality Court," the commission says in a statement.
"The commission is deeply concerned by the ongoing public statements by political leaders and members of the public which have the potential of causing harm to the right to security of person.  They also damage social cohesion and undermine national unity in this country.

"Freedom of expression is important and indispensable to our constitutional democracy.  While the commission will continue to promote and vigorously protect this freedom, it should be noted that the right is not without limitations," it says.
The commission believes Mngxitama's comments go beyond freedom of speech.
"Hence the decision to institute action in the Equality Court against him.
"The Constitution recognises that systemic inequalities and unfair discrimination remain deeply embedded in our social structures, practices, attitudes and institutions."

Source: Jacaranda FM