The school was thrust into the spotlight in October when 87 young pupils alleged that they were sexually assaulted by a scholar patroller. The patroller's case is before court.
Gauteng department of education spokesman Steve Mabona last night said the cop's duty was to interact with the affected pupils to get information on the alleged abuse.
"[The police officer] then compelled the two learners to undress while in a class [where all the children who had been abused were being interviewed] and then he allegedly molested them.
"By law he raped them because he fingered them and then he said to them, 'don't tell anyone'."
Mabona said the department was notified by the parents of the alleged victims.
"They asked if what the cop did was part of the procedure when evidence was being gathered and we said no."
Independent child protection consultant Joan van Niekerk said: "It's a terrible violation [because] it compounds the original trauma.
"It makes it so much worse because these kids will not know who to trust because this person was supposed to help them and support them has now abused them.
"I would regard this case as the most serious ."
One of the parents of the 87 victims told Sowetan she was saddened by the latest sexual abuse allegations.
"I've reached a boiling point because there are people who are accusing us [parents] of seeking attention.
"My aunt told me that while I went to the police station to open a case, there were people at the school who said, 'this can't be true, these parents just want to make it to the news'," said the parent of a seven-year-old pupil.
Lesufi said in statement that a sexual assault case was opened against the police officer by the parents at Orlando police station.
"It is unfortunate and regrettable that this incident occurred to the very same learners who were previous victims of the school patroller, in the hands of someone entrusted to ensure their safety."