Gauteng Education MEC Panyaza Lesufi said an intensive investigation into the matter was under way.
He revealed that‚ while a grandparent of one pupil had laid an official complaint with the school in September‚ the school had only submitted a report on the incident to the department in October.
"We have already quarantined the school leadership. They are under heavy investigation. It is a serious omission on their side‚" said Lesufi.
"I visited the school yesterday and I got a report from the school leadership. An independent team has been appointed to verify the information we have received on the report‚" he added.
The Private Security Industry Regulatory Authority said it was probing whether the accused was registered with them and would take the necessary action.
Lesufi‚ however‚ explained that it was the security department that was behind the screening of security officials deployed to schools.
He said a broader investigation has been instituted to see whether the man has previously been deployed to other schools and whether he was embroiled in any such allegations there.
"I must apologise to the parents. I am disgusted … Schools should be the safest place for our children‚" he said.