The Australian Christian Lobby (ACL) has called for education minister Christopher Pyne to strip the Safe Schools Coalition of its funding.
In a press release, the ACL said the program promotes "radical sex experimentation" that is inappropriate for Australian schools.
The Safe Schools Coalition (SSC) is a program that aims to combat bullying of LGBTI students and make schools a more inclusive environment. It is funded by the federal department of education.
"No one should be bullied at school, including children grappling with same-sex attraction or gender confusion," said ACL spokesperson Wendy Francis.
"But promoting radical sexual and gender theories to children without parental consent is not the role of the Federal or State Governments."
The ACL points to examples of SSC material they believe is inappropriate, including a resource explaining that there are many different ways of having sex.
Francis described the resources as "extreme sexual material" that contributes to the over-sexualisation of society and strips children of their innocence.
Other resources advise schools on how to best help transgender students feel safe, explaining that they should be able to wear uniforms and use toilets that they feel comfortable in.
"Girls' toilets should always be a safe place for them and should be off limits to a boy who might be transitioning into a girl," said Francis.
Kate Doak, SSC federal board member, slammed the ACL's call for the program to be defunded.
Claims that the organisation promotes "radical sex experimentation" and sends an inappropriate message are sorely misguided, Doak told BuzzFeed News.
"The SSC is there to help kids, to find out about these things and feel less alone," Doak said.
"We've seen monumentally high rates of suicide among the LGBTI community. The impact of programs like Safe Schools can go towards helping this."
Doak said the resources and support offered by SSC are "much needed" – in particular, when it comes to understanding transgender students.
"Not all schools would have access to these resources if it weren't for organisations such as Safe Schools. It's an entity that is needed," she said.
"The ACL's press release actually shows us why we need programs like Safe Schools."
Christopher Pyne's office has been contacted for comment.