The image from Laerskool Schweizer-Reneke kindergarten in the north west of the country shows a group of 18 white pupils in the foreground.
North West MEC for Education Sello Jonas Lehari was to lead a team of senior management to Laerskool Schweizer-Reneke to Thursday to investigate allegations of racism.
The outcome was that the teacher allegedly responsible for separating the children has been suspended with immediate effect, reports eNCA.
A shocking photograph of black and white primary school children sitting separately in a classroom has provoked widespread anger.
He said the school's explanation was that black children were separated because they were new at the school and could not speak Afrikaans or English.
In a statement, the Schweizer-Reneke school says that the photo is a reflection of a single moment in a grade R classroom.More news: Kelly Manager For Threatening Victims Father
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Image copyright. Image caption After a backlash from parents the school reportedly shared this picture of the children sitting in integrated groups What has the response been?
Activist and ANC campaign manager, Mcebo Dlamini, wrote on Facebook: 'What is most provoking about this image is not that black kids are ostracised from white kids, that is common in our supposedly post-apartheid Africa.
Speaking to News24, education department spokesperson Freddy Sepeng said officials were still locked in a meeting at 12:00.
"If there is racism in any of our schools, that should be attended to as quickly as possible. He will be looking into the matter of the principal also".
He added: "We are suspending her [the teacher] because we want the investigation to be fair and free".
There have been calls to shut down the private school while others said it was proof that racism was still rampant in everyday life across South Africa. However, based on our understanding and the video you will see below, things have intensified outside the school, where protesters, dressed in political regalia, have picketed, chanting angrily and climbing the school's fence.