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 the age of 16.

The student's lawyer, Judy Courtin, said the removal of senior staff at the prominent 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 told AAP.

St Kevin's dean of sport Luke Travers, who also gave Kehoe a reference, has also been stood down, pending an investigation.

Dr Courtin said it was upsetting that it took a lengthy legal process, a conviction and the shaming of a student for action to be taken.

"It's taken a school to basically blame the victim, and the victim to suffer very serious psychiatric harm," she said.

"It's taken battle after battle ... and taken this young man who is still recovering to have the courage to go public."

Dr Courtin added "the truth should have been acknowledged and acted on from day one."

In a letter issued to parents on Wednesday, Mr Russell said students' wellbeing was his biggest priority and "the current situation means that the best way to achieve this is to resign".

A spokesman for St Kevin's said the resignation was effective immediately.

Mr Russell's letter did not directly address the controversy.

He had provided the reference for Mr Kehoe who received a two-year community corrections order and 100 hours of community work, with a sex offender registration order granted in 2015.

Edmund Rice Education Australia (EREA), the governing body of St Kevin's, said current St Patrick's College, Ballarat principal John Crowley would take over as headmaster until the end of the school year.

The letter added that two other unnamed teachers also currently under EREA investigation are not at the school.

"EREA accepts the gravity of the matters raised in recent days," the statement added.

"Business as usual is not an option for St Kevin's in response to these issues, which need to be addressed as a matter of priority.

"It is clear that what has occurred has fallen short of what the community expects, and what we expect of ourselves.

"Importantly, it must be stated that we find the crimes of Peter Kehoe abhorrent and we strongly condemn all behaviour of this nature."

Also on Wednesday, St Kevin's sister school Sacre Coeur announced it had placed all their upcoming partnership programs on hold while the state government's education regulator conducts an investigation.

The regulator is looking into whether St Kevin's complies with child safety standards.

Australian Associated Press