The state's highest court has found the Christian Brethren church discriminated against a suicide prevention group for young gays when one of the church's youth camps refused to take a booking from the group.

Court of Appeal president Justice Chris Maxwell and Justices Marcia Neave and Robert Redlich said Christian Youth Camps (CYC), owned by the Christian Brethren church, were opposed to homosexual sexual activity, as they considered it "contrary to God's teaching as set out in the Bible".

The Christian Brethren church is historically linked to the infamous Exclusive Brethren, but broke away in the mid-1800s.

In a majority decision handed down on Wednesday, Justices Maxwell and Neave dismissed CYC's appeal against a Victorian Civil and Administrative Tribunal finding that a Phillip Island youth camp run by CYC had breached the Equal Opportunity Act by refusing to take a booking from members of Cobaw Community Health Service's Way Out project.

The Way Out project is a statewide youth suicide prevention project targeting same-sex-attracted young people in rural areas.