A black parent told the TimesLive news site that she thought her child's first day at school in had got off to a good start until she saw the image.
He confirmed the teacher involved in the incident had been suspended.
A South African primary school teacher was suspended on Thursday after a photograph appeared to show black children sitting separately from white children in a classroom, sparking a storm of racism accusations.
Provincial education minister Sello Lehari said the teacher's explanation was that "the learners were separated according to those who could understand Afrikaans and English".
"This was meant to be an exciting day for me, but it's not", she said.
"But I am pissed off", said the mother, who said she was not sure what further steps to take. "Around 9 o'clock the class teacher posted the picture saying they are settling well at school".
The image, which rapidly spread across social media, showed about 17 white children sitting around a large table, with four black children around a small corner table in the background.
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".
'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'. "Now they want to make this as if its racism, everyone just wants to make white people racists, we are not racists, we just want what was best for our children", the parent said.
"We often visit the school to hold workshops and I have never seen black people playing with their white peers".
One white parent said: "If you are not happy here‚ take your child to another school‚ nobody is forcing you".
Concerned resident Lebogang Motlhabane claimed that black children were often denied access to the school and were placed on waiting lists when they applied for enrolment.
"I remember in 2008‚ we left township schools at that time and protested at this school because we wanted this [racial segregation] to end as this is also a government school‚" one resident said.