St Kevin's College deputy principal Janet Canny has been stood down following allegations she responded inappropriately to a teacher's complaints about further child-grooming allegations.
Edmund Rice Education Australia confirmed on Thursday that Ms Canny had been removed from her position.
The Melbourne Catholic boys' school is set to undergo more scrutiny after teacher Maree Keel alleged she was mistreated and has launched legal action under the Fair Work Act.
"Ms Keel alleges she was mistreated after raising concerns about the behaviour of a St Kevin's staff member," law firm Maurice Blackburn said.
The ABC reported on Wednesday that St Kevin's allegedly responded inappropriately to Ms Keel's complaint about inappropriate sexual conduct by a fellow teacher last year.
Ms Canny told Ms Keen she was being "disloyal to St Kevin's College", the ABC said.
St Kevin's College deputy principal Janet Canny has been asked to step aside amid an investigation at the school. Source: EREA
St Kevin's headmaster Stephen Russell resigned on Wednesday over the school's handling of a 2014 child-grooming case.
Mr Russell had been under pressure after it was revealed he provided a character reference to a court for former volunteer athletics coach Peter Kehoe who was convicted of grooming a student under 16.
Premier Daniel Andrews said St Kevin's parents had every right to be unhappy with Mr Russell's actions and welcomed his resignation.
"If he'd been a principal at a government school, I wouldn't have had confidence in him. So I think that parents at St Kevin's have got every reason to be not pleased by his conduct, (but) perhaps pleased by his most recent decision."
Outgoing principal Stephen Russell. Source: St Kevin's College
St Kevin's dean of sport Luke Travers, who also gave Kehoe a reference, has also been stood down, pending an investigation.
The lawyer of the student who was groomed by Kehoe, Judy Courtin, said the removal of senior staff at the prestigious Catholic school showed a "shift in the power base" between victims and institutions.
"Power was in institutions. This shows survivors are not willing to give up," she said.
St Patrick's College Ballarat principal John Crowley will take over as headmaster on Friday until the end of the school year.
The St Kevin's spokesman said Mr Crowley would decide who his deputy would be.
