The department said the appointment was made according to procedure.
Parents at the Soweto school have accused the department of appointing a new headmaster without their consent.
Department spokesperson Steve Mabona said: "The responsibility of appointing a principal rests with the SGB. The SGB went through the process of shortlisting and had the to interview the shortlisted candidates."
However, parents at the school have rejected the department's version.
Parents at the school say they feel disrespected by the appointment of a new principal, as the acting headmistress was doing a good job and there was no reason to remove her.
In a statement, they refer to the new headmaster as "a Bantu African" but insist they are not rejecting him on the basis of race.
The principal was supposed to start his first day on Friday, two years after his predecessor was sacked amid a circumcision scandal.