North West MEC for education and sport development Sello Jonas Lehari and senior managers in the department will on Friday conduct an intensive investigation into the separation of pupils at Laerskool Schweizer-Reneke based on race.
This comes after an image that has gone viral on social media showing a racially divided Grade R class at the North West primary school sparked outrage across the country.
"The North West provincial government condemns any form of racism in the strongest possible terms and deeply regrets this unfortunate incident 25 years into the democratic dispensation," Vuyisile Ngesi, spokesperson in the office of the premier, said in a statement on Thursday.
TimesLive reports that the image was first shared on the school's WhatsApp group.
"This was meant to be an exciting day for me but it's not," a parent of one of the black Grade R pupils told TimesLive.
"All I saw was messages from the white parents saying 'dankie, dankie' (thank you, thank you') on the WhatsApp group but no one was saying anything about the separation of the learners," said the mother who was not named to protect the identity of the child.
The provincial department of education and sport development has since sent a team to establish the circumstances that led to the children being separated according to race.