Arguments erupted at the new multimillion-rand Seven Fountains Primary School built by US talkshow queen Oprah Winfrey in Kokstad.
Local parents were determined to get their children enrolled at the school.
The school governing body (SGB) said not everyone could be accommodated.
Parents claimed that their kids were turned away because of the high number of children trying to get into the school.
Some parents exchanged harsh words with members of the governing body, accusing them of favouritism.
SGB member Kholeka Nduli denied the allegations, claiming that the governing body wanted to avoid overcrowding at the new school by ensuring that other schools also had pupils.
"What we have noticed is that some children were leaving their schools to enrol here because of the beauty of the school, and not because their schools were full," Nduli said.
She said a principals' meeting held on Saturday to discuss enrolment took a decision to regulate the admission of pupils.
Nduli denied that some pupils were told to go away, saying they were put on a waiting list.
Shayamoya councillor Willem Bhengu confirmed that the school started classes yesterday.
It has 24 classrooms, a fully equipped computer laboratory, a multi-purpose centre, teachers' accommodation and sports fields. The school will be run and controlled by the Department of Education.
Winfrey built the school when more than 400 children were left stranded after local farmer John Borrowdale demolished their school.
Ntokozo Maphisa, of the Department of Education, said there was nothing the department could do if the school was full.