For the first time, a Catholic schools network is rolling out an alternative to Safe Schools which it believes will train teachers to stamp out homophobia and transphobia.

Edmund Rice Education Australia has distributed resources to its 52 schools and will soon run training to help teachers create a safer and more inclusive environment for gay and transgender students and LGBTI families.

The training material states that children may have a sense of their sexual orientation in early primary school and teachers must support them so they can develop "a positive self-identity".

The organisation's executive director, Wayne Tinsey, said the Catholic education sector and church had been "silent" for too long.

"We are not trying to be provocative and we are not trying to create divisions," he said.

"Our core belief is that of inclusion – bullying, harassment and discrimination totally contravenes that and has no place in our schools."

Teachers will also be coached to respond to concerns from parents who may not want schools to address homophobia because of their Catholic beliefs, or might accuse schools of promoting a "homosexual agenda".

"Schools and teachers who address LGBTI educational issues are not advocating or promoting a homosexual agenda; they are creating a safe, caring and inclusive environment in which all students and their families can expect to be treated with dignity and respect," it reads.

Gerald Bain-King, principal of one Edmund Rice school, the Christian Brothers' College in St Kilda, said the initiative would allow Catholic schools to have more effective conversations with young people who may be coming to terms with their sexuality. 

"We have had a number of same-sex attracted students at our school and have always tried hard to accommodate them," he said. 

"This gives young people and their families a sense of security because they know how the issue will be dealt with."

The new approach follows Catholic school authorities deeming material in the Safe Schools initiative inappropriate.

The federal government will stop funding Safe Schools in June, but in Victoria the initiative will continue to be funded by the state government and all state secondary schools must sign up by the end of 2018.

"It's not just enough to critique other models, we need to provide a realistic alternative for our teachers," Dr Tinsey said.

It calls on staff to highlight that the Catholic church teaches that "every person is made in the image and likeness of God and therefore has an inherent dignity."

Dr Tinsey said schools had been crying out for help, and five transgender students in Edmund Rice schools were currently transitioning. 

About 16.8 per cent of high school students are same-sex attracted or bisexual, according to research quoted by Edmund Rice.

These students experience high levels of bullying which may lead to self-harm, drug abuse and disengagement from school.

He does not expect any backlash and is in talks with Catholic bishops about sharing the resources.

"This is about upskilling teachers in the way they get skilled up in other areas like domestic violence," he said.

It comes as Catholic Education Melbourne reviews anti-bullying policies for Victorian Catholic schools with assistance from its new "safe and supportive learning communities reference group". 

Former principal Paul Tobias, who is on the reference group and was also involved in developing the Edmund Rice resources, said Catholic teachers were previously unsure how to support these students because of the Catholic church's teaching about same-sex attraction. 

"This provides clarity," he said.

Mr Tobias, who retired last year as principal of  St Joseph's College in Geelong, said a homophobic culture negatively impacted all students.

"You end up with a narrow gender stereotype that everyone is trying to conform to – a hyper masculine culture that promotes sport at the expense of everything else."