The Catholic boys school at the centre of a grooming scandal is facing fresh allegations it mishandled concerns about inappropriate sexual conduct by a teacher towards a student.

Key points: A new allegation of inappropriate sexual conduct by a St Kevin's teacher towards a student has been revealed in court action

A new allegation of inappropriate sexual conduct by a St Kevin's teacher towards a student has been revealed in court action The former head of counselling, Maree Keel, alleges she was told she was being "disloyal to St Kevin's College"

The former head of counselling, Maree Keel, alleges she was told she was being "disloyal to St Kevin's College" Ms Keel's lawyer claims the school's deputy head had "obstructive involvement" in three mandatory reporting incidents

The headmaster of St Kevin's College in Melbourne has resigned and the school's dean of sport has been stood down following a Four Corners investigation into the college's response to the grooming of a student by a former athletics coach.

The Toorak school has been in damage control since Four Corners revealed headmaster Stephen Russell and the dean of sport, Luke Travers, provided references for convicted child sex offender Peter Kehoe, but did not support the victim during the court process.

Now, there are also allegations about how the college's deputy head, Janet Canny, handled a complaint about alleged sexual misconduct by a teacher towards a child.

The former head of counselling at St Kevin's, Maree Keel, alleges the college responded inappropriately and inadequately to a complaint she made about inappropriate sexual conduct by a teacher in 2019.

Deputy head Janet Canny is facing allegations she responded inappropriately to a complaint. ( Supplied )

In an action filed in the Fair Work division of the Federal Court on Wednesday, Ms Keel claimed she became aware of the inappropriate conduct in August 2019 and had a legal obligation to report it under mandatory reporting guidelines.

Ms Keel's lawyer, Josh Bornstein, said the allegations of grooming behaviour were over a period of two years in 2018 and 2019.

"My client sought to agitate them in mid-2019 and found she was being impeded and then subjected to all sorts of adverse conduct herself," Mr Bornstein said.

"The teacher about whom she made the complaint of grooming behaviour, was also the subject of other concerns at the school in relation to other matters of a similar nature … so potentially the issue was bigger than what my client first thought."

'Disloyal to St Kevin's College'

Ms Keel also alleges that in a meeting about the issue, Ms Canny told her she was being "disloyal to St Kevin's College" and "unwilling to co-operate with St Kevin's College leadership in the same way as her predecessors".

"Ms Keel stated to Ms Canny that she was concerned about Ms Canny's obstructive involvement in three mandatory reporting incidents that year," the statement of claim said.

Mr Bornstein said Ms Keel felt under enormous pressure "not to make the complaints to authorities, not to fulfil her obligations under mandatory reporting legislation, which is very strict, and that created an untenable situation for her".

Ms Keel also claims Ms Canny described her as "uncooperative and vexatious" and threatened to reduce her hours and abolish her role.

The former counsellor wants the St Kevin's College leadership team to undertake training in mandatory reporting compliance. ( Four Corners )

In November, the complaint alleges, Mr Russell offered to double her long service leave entitlements to 30 weeks if she agreed to resign.

Later that month, the role of head of counselling was abolished.

Ms Keel has been absent from work due to illness since that date.

The claim alleges Edmund Rice Education Australia (EREA), the governing body overseeing St Kevin's College, breached the Fair Work Act by threatening to reduce her hours, threatening to abolish her role and engaging in bullying conduct.

Ms Keel is seeking both compensation and an independent investigation into her allegations of Ms Canny's "obstructive involvement" in mandatory reporting.

St Kevin's has been in damage control since a Four Corners investigation revealed how it handled a grooming case. ( Four Corners )

She's also seeking an order for EREA to compel members of the St Kevin's College leadership team to undertake training in mandatory reporting compliance.

"She feels very distressed at what's unfolded," Mr Bornstein said.

"She's been part of the school community. She's been part of Catholic education for a very long time, very respected in the field of student counselling, very committed to the kids and welfare … it has caused her immense stress and damaged her health.

"She wants to change the culture and St Kevin's."

EREA is yet to file a response to the statement of claim.

St Kevin's College and EREA have been contacted for comment.

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Two current teachers under investigation

Numerous current and former staff, students and parents from St Kevin's College told Four Corners the school had a history of failing to adequately deal with complaints of inappropriate behaviour.

Those complaints included an allegation of sexual harassment and concerns raised by staff members about potential grooming and inappropriate behaviour towards boys by two male teachers.

Following the investigation, on Tuesday the Victorian Government announced the state's education regulator would investigate whether St Kevin's College was compliant with child safety standards.

St Kevin's College had previously declined to answer questions regarding complaints about current teachers.

"Two teachers who are currently under EREA investigation, are also not presently at the school until further notice, until those investigations are complete," EREA executive director Wayne Tinsey said in a statement.

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