The Laerskool Schweizer-Reneke teacher at the centre of alleged racism in a classroom has been suspended with immediate effect.
The education minister for the North West province, Sello Lehare, said the school explained that "the learners were separated according to those who could understand Afrikaans and English", the BBC reported.
"When I got to the class before school in the morning, all the children's names were already written on the desks they were supposed to sit at".
In the other pictures, children of different races can be seen interacting with different pupils in different seats.
A parent of a student in the photo told the outlet she thought her child's first day at school had started well until she saw the image.
"I will send a team to do an investigation into all schools.to deal with issues of racism in totality", Lehari said.
The Afrikaaner children who are greater in number, are seated at a long table, in the center of the shot. "If they are not happy‚ let them take their children there".
The teacher also complained about the school's language policy.
She claimed the white children did not have the same experience.
She said no one said a thing about the separation of the grade R class, so, she spoke to another parent outside of the WhatsApp group.
Or, as many people have suggested, how this was all due to the fact that the parents of the four black children may have registered their children late and how this is, indirectly, their fault.
Some white parents on Thursday took their children away from the school after protesters gathered outside.
An education official said: 'We are not sure whether is fake or real, if it's real we are condemning it, we say not during this era, we can not really accept it'.
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.
"We saw the photo and we were also angered by what we saw", Jozeph du Plessis, chairman of the school's governors, told the eNCA television channel.
"The governing body does not condone any distinction based on race".
He said that the school would help staff in "aspects where it appears that integration is not taking place as it should".
Earlier, parents had to fetch their little ones after protests became heated outside the school.
While the picture has sparked outrage others have pointed out that the it was seemingly part of a series of pictures taken on the same day in the same class.