A mother of one of the black learners was quoted as saying: "This was meant to be an exciting day for me but it's not".
The principal at the school said she was that she was not aware of the situation.
A teacher at Laerskool Schweizer-Reneke, the school caught up in a race controversy, was suspended after government officials visited the school on Thursday.
Local authorities say they "highly condemn" the incident and have removed the teacher "pending investigation".
"We want the SGB (school governing body) of the school to also account, including the MEC, Mr Sello Lehare, to account because education falls under him".
The school is being accused of racism after a photograph emerged showing a group of white pupils sitting together while their four black classmates sat at a small table near the door.
Parents had dropped their children off on Wednesday morning for their first day of school at Schweizer-Reneke primary school.
According to local media, the picture was shared by the class teacher on the school's WhatsApp group.
"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 fuming mother.
Meanwhile, the picture has since gone viral on social media.
"We did not accept the explanation", he told community members who were protesting outside the school today.
You can take your kids to the whitest schools in the country but so long as the black majority is poor, your kids will always be reminded that they are black and therefore inferior.
Curro Foundation School in Roodeplaat was found guilty of racism after a probe by the Gauteng education department.
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.
The statement by the school does not, however, give a reason why the children were seated the way they were.