Victoria's most senior Catholic said he did not want the church's schools to accept and tolerate that some students were gay.
Denis Hart, the Archbishop of Melbourne, made the comments in 2007 after he buried a report designed to address homophobia, discrimination and self-harm in Catholic schools.
And in May this year, Archbishop Hart asked Catholic school principals to send children home with glossy booklets opposing same-sex marriage.
This week Archbishop Hart appeared to distance himself from the comments, saying there was no place for homophobia and everyone should be respected. But he said the church would never promote "the gay lifestyle".
The Not So Straight report by Jesuit Social Services was aimed at helping teachers respond to the needs of gay teens in Catholic schools. It highlighted high levels self harm, and even suicide, among same-sex attracted students.
The report's author, former Jesuit priest and now RMIT Professor Peter Norden, used the material to train Catholic school principals across Australia.
But letters obtained by Fairfax Media reveal that Archbishop Hart prevented the report from being distributed or workshopped with schools in his diocese.
Archbishop Hart said in a 2007 letter to Professor Norden that the report should not be distributed because it could "create a situation whereby it is accepted and tolerated that a proportion of our young people do not have a heterosexual orientation".
In a separate letter he raised concerns about the report's use of the term "natural behaviour" to describe a gay student.
"Both the text of the report and the case studies, either blur the clear position of the church or by the use of terms such as 'natural behaviour' imply a suggestion that alternative sexuality should be accepted as part of the scene," the archbishop said.
Professor Norden – who was made an Officer in the Order of Australia for services to the mental health sector and the Catholic Church – said the archbishop had denied same-sex students a duty of care by "turning a blind eye".
"There is an element of both denial and discrimination in relation to same-sex attracted students and their families," he said.
"It concerned me that the archbishop repeatedly refused to meet with me to discuss the report, despite it being warmly received in every diocese in Australia, including Ballarat, Sandhurst and Sale."
He said same-sex attracted students in the Catholic school sector were particularly at risk because of the "moral overload" that stemmed from the church's messages about "depraved activity".
He called on the Catholic Church to develop a positive understanding of sexuality.
Archbishop Hart said the report was not released to schools because it failed to clearly address the teachings of the Catholic Church.
He said same-sex-attracted children attended Catholic schools and individual schools determined what support was needed for students.
"The church would never promote the gay lifestyle, but importantly would see loyalty to one partner as being vital within the morality of church teaching."
In May this year, hundreds of children were sent home with a 15-page booklet, titled Don't Mess with Marriage following a request from Archbishop Hart.
The booklet said it was important for children to have a mother and father, and redefining marriage would have "far-reaching consequences".
"'Messing with marriage', therefore, is also 'messing with kids'."
St Joseph's College, a Christian Brothers secondary school in Geelong, has worked hard to transform its previously homophobic culture.
In 1998, principal Paul Tobias set up a homophobia taskforce after the school received a letter from a former student who spoke about how he was bullied for being gay.
Stamping out homophobia had benefited same-sex attracted students, and the broader school community, who no longer felt restricted by "narrow male stereotyping".
Mr Tobias said there was a tension between church authorities and schools when it came to same-sex attracted students.
"Any Catholic educator who is doing work in this area can expect there is a fine line you walk. If someone perceives that if you are doing work in this area, you are seen as promoting a lifestyle."
He said it would be useful if the Catholic sector adopted a policy to explicitly meet the needs of same-sex-attracted students. This would ensure they were educated in a safe environment.
St Joseph's is one of only two Victorian Catholic schools that has signed up to the Safe Schools Coalition, which runs programs to ensure schools provide a safe environment for same-sex attracted, gender diverse and intersex students, teachers and families.