North West MEC for education and sport development Sello Jonas Lehari and senior managers in the department will on Thursday conduct an intensive investigation into the separation of pupils at Laerskool Schweizer-Reneke based on race.
Meanwhile, the North West education department said it would return to the school next week when it received the outcomes of its investigation.
The parent said: "This was meant to be an exciting day for me but it's not".
Four black children sat at a small desk in a corner far from 18 white kids who occupied one big desk in the middle of a classroom at Laerskool Schweizer-Reneke.
When parents then complained to the school, according to TimesLive, they were sent a different picture after the children's break showing that they had been "moved to different seating spaces to ensure they were not separated according to race".
School leaders have now launched a racism probe after the picture, taken by a class teacher, emerged.
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?
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Student activist Mcebo Dlamini wrote on social media the "most provoking" aspect of the image "is not that black kids are ostracized from white kids, that is common in our supposedly post-apartheid Africa", South African news website TimesLIVE reported.
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.
But he said the blame must lie with the Government, which had 'neglected public and rural schools'.
In a statement on Wednesday, the National Freedom Party (NFP) called for the shutdown of the school saying it strongly condemned the racist segregation of learners.
The mother, who is not being named to protect the identity of her child, said earlier that her child's first day started off smoothly.
The school hasn't responded to requests for comment.