The deputy principal of St Kevin’s College in Melbourne, Janet Canny, has stood down following allegations she mishandled a complaint about the behaviour of another staff member, pressuring the person who made the complaint to remain silent.

A statement issued to the school community by Edmund Rice Education Australia on Thursday morning said: “Mrs Canny strongly refutes these allegations.”

The statement said Canny “has been asked to step aside from her duties pending an investigation into allegations regarding her handling of a staff member’s complaint”.

“The investigation will receive the highest priority and be conducted by professionals external to the college and Edmund Rice Education Australia.”

Law firm Maurice Blackburn is representing the school’s former head of counselling, Maree Keel, who alleges Canny told her she was being “disloyal to St Kevin’s College” when Keel made a complaint about a teacher’s inappropriate sexual conduct in 2019.

“Ms Keel alleges she was mistreated after raising concerns about the behaviour of a St Kevin’s staff member,” a statement from Maurice Blackburn said.

On Monday the ABC’s Four Corners program revealed the college’s headmaster, Stephen Russell, wrote a character reference for a school’s volunteer athletic coach after he was convicted of grooming a student under the age of 16. Russell resigned on Wednesday, and has been replaced by the principal of St Patrick’s College Ballarat, John Crowley.

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 said.

In a statement of claim filed to the federal court in Melbourne’s fair work division, Keel alleges she was obliged under mandatory reporting laws to report her concerns about a staff member, only to be told by Canny that she was being “disloyal” and demonstrating that she was “unwilling to cooperate 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.

In a second statement issued later on Thursday, Edmund Rice Education Australia said James Daly had been appointed acting deputy of St Kevin’s College, and would also be the interim senior child safety officer and a key point of contact for staff and parents in relation to any child safety concerns.

“We urge staff, students, parents, Old Collegians and others to come forward with any information at any time with assurance that they will be supported and protected,” the statement said.

Victoria’s education minister, James Merlino, has said the state’s education regulator, the Victorian Registration and Qualifications Authority, will review the school’s management of child abuse risks.