"The staff member has been stood down, and we are working with the school as they support their students and staff ... we will work with the school for as long as they need us.
"The principal and the board are currently working with a range of agencies including the police, and are focused on preparing for the start of term three."
The staff member was a counsellor working at the school when the alleged offending took place.
The criminal charge comes after a number of sexual abuse cases against minors in the Far North.
The most high-profile was that of former Pamapuria School deputy principal James Parker, who is serving preventive detention on more than 70 sexual abuse charges involving 20 victims from the school.
An inquiry into Parker's employment and sexual offending led to an Education Review Office report into the safety of students in schools. Released in January, it found that a third of schools were unlikely to recognise situations when students could be at risk from staff and respond appropriately.
Ms Casey said schools were required to police-vet potential employees, and were responsible for hiring staff and teachers.