This was after a picture showing black pupils sitting separately from white pupils at a North West school went viral on social media.
Parents have started removing their children from a Schweizer-Reneke primary school in the North West amid protests outside the school reports EWN.
"On behalf of the department, I wish to condemn in the strongest terms any allegation of racism in our schools which contradict the constitution of our country", North West education and sport development MEC Sello Lehari said.
The picture was shared on the school's WhatsApp group by the children's class teacher.
"All I saw was messages from the white parents saying "dankie, dankie ['thank you, thank you"] but no one was saying anything about the separation of the learners", she told the South African Times.
Earlier, parents removed their children from the school and tensions were high as EFF members gathered outside the school.
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"What is most provoking about this image is not that black kids are ostracized from white kids, that is common in our supposedly post-apartheid Africa".
"Rather what becomes painful is that there are black people who still insist that racism has ended and who think that blacks and whites can have peaceful relations that do not have undertones of racism". "Learners from different backgrounds, including race, religion and language, are not merely accommodated but are fully integrated in all aspects of the school environment".
"The barbaric conduct displayed by private schools of racial segregating children is equally the same as giving innocent children experience of an apartheid system", said the NFP, which urged the [African National Congress] ANC-led government to ensure that it improves the conditions and quality of education at public schools.
In 2015, a year before the incident that took place in Pretoria, the Gauteng Department of Education (GDE) found Curro Roodeplaat School guilty of racism after a video surfaced online of children being separated based on the colour of their skin.
The school hasn't responded to requests for comment.