Some chaplain providers have been linked to homophobic views, and critics claim the government's decision to scrap funding for secular student welfare workers is directly at odds with its funding of the Safe Schools Coalition, to be rolled out nationally on Friday.

The program helps schools stamp out homophobia and celebrate diversity through moves such as same-sex formals, gay-straight student alliances and expanding reading lists to include books with gay and lesbian narratives, including Brokeback Mountain and Stone Butch Blues.

Scott Hedges, co-founder of Fairness in Religions in School, said the push to protect gay pupils, who are up to six times more likely to contemplate suicide than their straight peers, was irreconcilable with the chaplaincy scheme.

While parliamentary secretary for education Scott Ryan has insisted chaplains are banned from proselytising, Mr Hedges pointed to recent revelations in the The Sunday Age that found that a volunteer for Access Ministries - which supplies chaplains and religious instruction to more than 300 Victorian schools - had distributed ''Biblezines'' to year 6 students at a Torquay school, claiming homosexuality is a sin and urging those who think they are gay never to act on it.

''On one hand, you have the government backing the Safe Schools program that is affirming the normality and acceptability of homosexuality, and on the other hand they are funding a group like Access Ministries, purporting to represent 12 churches, some of which may be progressive but some of which are openly hostile to homosexuals and have a theological position against homosexuality,'' he said.

More than 140 schools have signed up to the voluntary Safe Schools scheme, which began in Victoria and will be expanded to NSW and South Australia, with a target of 100 new schools within six months. Funded by the federal Education Department and run by the Foundation for Young Australians, the initiative was spearheaded by former Labor finance minister Penny Wong, and inherited by the Coalition.

It comes as a study by the Young and Well Co-operative Research Centre revealed two-thirds of non-heterosexual young Australians have been bullied about their sexual orientation, and school was the most threatening place.

Safe Schools program director Sally Richardson would not comment on the chaplaincy scheme but expected any chaplain or staff member to encourage young people to be themselves.

There is growing concern about the chaplaincy program, which was allocated $245 million in the federal budget, with an online petition launched by gay and lesbian movement All Out, attracting 180,000 signatures.

Associate Professor Anne Mitchell, chairwoman of the Safe Schools steering committee and a La Trobe University expert on same-sex attracted youth, said many felt rejected by religion and this would make them less likely to seek guidance from chaplains. ''One of the antidotes to suicidal thoughts for these kids is talking to someone and being accepted. Feeling that there's somebody at school you can go to is so important,'' she said.

Mr Ryan said in a statement that a code of conduct required chaplains to ''respect, accept and be sensitive to other people's views, values and beliefs that may be different from their own''.

jstark@fairfaxmedia.com.au