ACL said the program, run by Safe Schools Coalition Australia, promotes "radical sexual experimentation", and argued that its $8 million federal funding should be withdrawn.

More than 350 Australian schools are signed up to receive the Safe Schools program, including two colleges, eight high schools and two primary schools in Tasmania, none of which are from the North.

Working It Out (WIO) executive officer Susan Ditter said the program existed to make sure all young people felt safe at school, and provided another avenue of support for same-sex attracted or transgender individuals and their families.

The opt-in program offers support and training to schools, teachers and lesbian, gay, bisexual, transgender and intersex students.

WIO staff, several school chaplains and education department representatives received Safe Schools training in March, with the programs now being rolled out in schools.

"Our intent in delivering the Safe Schools program is to avoid any risks or mental health issues if children feel they have nowhere to be themselves," Ms Ditter said.

"As parents can testify, this program is not about sex education or sexualising anything or anyone. It is about inclusion and therefore it is about the right of children to be safe at school."

ACL spokeswoman Wendy Francis said the program denied a child's right to innocence.

"Our society is already over-sexualised without extreme sexual material and gender theory being promoted in schools," she said.

"Bullying for any reason is wrong and should be combated, but teaching primary school students about queer sex and cross-dressing without parental permission is not the way to do this."

The schools signed up for Safe Schools in the North West are Don and Hellyer Colleges, Ulverstone and Yolla High Schools, and West Ulverstone Primary.

The federal government has not publicly responded to the ACL's calls to withdraw the funding.