Paul Tobias, the outspoken principal of St Joseph's College Geelong, has called for an urgent review of the governance of Catholic primary and secondary schools.

"The Catholic Church persists with antiquated governance models which are no longer appropriate, rather than distribute power appropriately," he said.

In a strongly worded submission to the Royal Commission into Institutional Responses to Child Sexual Abuse, Mr Tobias said people who expressed different views to the church could "expect to be penalised, isolated or have their careers impacted".

Catholic bishops could also compromise the pastoral care of students, he said.

Mr Tobias, who is the only mainstream Catholic principal signed up to the Safe Schools Coalition, has been writing to the Catholic Education Office since 2004 to raise concerns about its lack of anti-homophobia programs.

"Principals like myself, who express a view in relation to the pastoral needs of young people in their care, risk suffering the cultural consequences implicit in the statement, "You are either one of us or you are not,' " he said.

Mr Tobias also spoke of the "muted response" he received from Cardinal George Pell – who was then Archbishop of Melbourne – when he apologised in 2000 to former students who had been sexually abused.

"The response from the then Archbishop of Melbourne, Cardinal Pell, could best be described as muted. I think at the time an apology was not considered as an appropriate response," he said.

It is rare for Catholic school leaders to openly criticise the Catholic church, but Mr Tobias, who has worked in the sector for 40 years, said he wanted to speak out. He is retiring at the end of the year.

He said Catholic principals had been largely silent throughout the royal commission – despite their schools being "prolific providers" of sex abuse victims.

"This silence does not indicate a lack of conviction but to me indicates a culture whereby those who are outspoken can expect the consequences," he said.

He also raised concerns about bishops appointing directors of the Catholic Education Office, sometimes without advertising the position. He suspects they appoint people who "tell them what they want to hear, rather than challenge them, especially around matters such as sexual abuse".

This led to issues being "glossed over", he claimed.

Unlike other states, parish priests in Victoria have a significant management role in Catholic primary schools.

Mr Tobias said this was an unsuitable role because priests had other work commitments and lacked expertise in education and the modern workplace.

"It can also mean that principals are pressured into positions and situations which they know to be inappropriate," he added.

Principals became "hopelessly compromised" because they relied on the parish priest for employment, he said.

Catholic Education Melbourne executive director Stephen Elder said the royal commission provided an opportunity for serious reflection on past practices.

"Learning from the mistakes of the past helps shape the future and our schools are united and absolutely committed to ensuring the terrible abuses of trust being examined by the Royal Commission into Institutional Responses to Child Sexual Abuse never happened again," he said.

Mr Elder said he did not want to pre-empt the details of the royal commission's recommendations and there would be much to learn from its final report.

He said that Catholic Education Melbourne had created wellbeing, child protection and professional conduct units, and schools were working to promote "safe, inclusive and respectful school communities".

Catholic Archdiocese of Melbourne spokesman Shane Healy said he rejected the concerns raised by Mr Tobias.

"The governance structures in place have served Catholic education and the many hundreds of thousands of students who have been and continue to be educated in Catholic schools very well."

He said the rollout of the building the education revolution and new child safe standards highlighted this "very successful" arrangement.