Rondebosch Boys High has come under scrutiny after a Whatsapp clip with racist lyrics was circulated at the school.
In the audio, one of the pupils is heard singing: "I feel unearthly pain because I hate k*****s" as he strums a guitar.
Two friends can be heard gasping after the boy sings the line twice, each time using the slur.
In a second audio clip, the boy apologises, while attempting to deny using the slur, saying: "I am not racist guys, I am not racist bro. I don't hate any races bra. I never say the k-word, it's just so mean."
School headmaster Shaun Simpson confirmed the incident.
"The boys have broken the law and the school's code of ethics. The correct procedures will follow where they will have access to representation ."
Two of the boys have withdrawn from the school and only one will face disciplinary charges .
Education Department spokesman Paddy Attwell said: "The department will continue to work with all principals, teachers and learners to promote the values of mutual respect and the constitution."