This was after a picture showing black pupils sitting separately from white pupils at a North West school went viral on social media.
The pupils were attending their first day at the Schweizer-Reneke school in North West province, and the teacher had taken a photograph to send to anxious parents.
However, while all the white parents were saying "dankie" (thank you), she noticed her child and three other black children were seated in the corner of the classroom while the white kids sat next to each other at a single large desk in the middle of the room.
"We want the SGB (school governing body) of the school to also account, including the MEC, Mr Sello Lehare, to account because education falls under him".
The school says that the photograph is not a reflection of the true character of the school.More news: Crystal Palace’s Wayne Hennessey denies ‘Nazi salute’ during team night out
Lehari said a decision on the fate of the principal had not been taken.
The picture of the children, aged four and five, was shared on a parents' whatsapp group to show them how the first day at school was going.
"As government, we would like to condemn any form of racism, alleged or not, and we deeply regret this unfortunate incident taking place in our country 25 years into democracy", said a spokesperson for the local government leader, Job Lekgoro.
The woman, who was not named, told TimesLIVE: 'This was meant to be an exciting day for me but it's not.
The statement by the school does not, however, give a reason why the children were seated the way they were.More news: Spain arrests players in match-fixing investigation
The parent, who preferred to remain anonymous, painted a grim picture of what transpired after she dropped of her 6-year-old at Laerskool Schweizer-Reneke.
The image began circulating on social media.
The removal appears to be as a result of fears surrounding safety, amid protests gathering momentum outside the school which appear to be led by EFF members.
'The barbaric conduct displayed by private schools of racial segregating children is equally the same as giving innocent children experience of an apartheid system'.More news: Rare 1943 copper coin could fetch a pretty penny in auction