Lesufi said the department had zero tolerance towards sexual misconduct and would take decisive action if the allegations were proven to be true.
"It is regrettable that such an unfortunate incident occurred in our environment, where learners must receive education, not abuse - especially from fellow learners," he said.
Lesufi said allegations that the principal of the school was having sexual relations with pupils were not substantiated.
He said pupil discipline had been identified as one of the department's priorities.
"We want cases such as school-based violence, gangsterism, drug abuse, cyber bullying and other related serious misdemeanors to be expedited, as well as [to] ensure that the department is proactive in identifying preventative strategies to eliminate these social ills from the school environment."