A national program to protect gay high school students from bullying and discrimination is being undermined by the federal government's chaplaincy scheme, say campaigners who fear religious counselling puts gay pupils at risk.

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 launched nationally on Friday.

Backed: Brokeback Mountain.

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 such as Brokeback Mountain and Stone Butch Blues.

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

While the government has insisted chaplains are banned from proselytising, Mr Hedges pointed to recent revelations in Fairfax Media that found a volunteer for Access Ministries - which supplies chaplains and provides religious instruction to more than 300 Victorian schools - had distributed ''Bible-zines'' 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 joined the Safe Schools scheme, which will be expanded to NSW and South Australia.