A prominent author and ethicist has called for an immediate freeze to school chaplain funding amid allegations a religious organisation is trying to make disciples of Victorian students.

Access Ministries, which received a funding boost in the federal budget, provides chaplains to 280 Victorian schools on the proviso it does not push religion onto students.

The organisation was today accused of breaching those guidelines after the ABC found a 2008 speech in which its head said chaplains "have a God-given open door to children" and "need to go and make disciples".

Access Ministries denies the claims, saying there have been no complaints it has breached any guidelines.

But Australian humanist of the year Leslie Cannold says the funding for school chaplains should be halted while the allegations are investigated.

"In the face of these persistent revelations that these organisations that provide chaplaincy services are taking advantage of the fact that children are away from their parents to try to convert them to Christianity, an immediate freeze on all the funds that are going to these organisations [is needed]," she said.

"In that pause, we would want the Government to re-check these programs, so if we are going to have pastoral care in schools and that is going to be funded by taxpayers, those people have no connection to any religion."

Federal Education Minister Peter Garrett has vowed to investigate the claims "if there is any indication or examples of that happening".

But Dr Cannold, who is also member of the Fairness In Religion In Schools group, says that is not enough.

"A very narrow group of Christian ministries are ... going [into schools] to try to reverse the decline in membership of the churches and get children converted to Christianity and make them active churchgoers," she said.

"These programs have been known [to do this] and have not been stopped by governments. It's been very hard to get the government to listen, even when there's been ample evidence that there is actually proselytising going on."

She says in many cases parents may not be aware school chaplains are in contact with their children.

"I think that is just a complete outrage. It violates ... our expectations about our rights as parents to raise our children as we see fit and not to have them preyed upon by religious ministries when they're at school," she said.

The chairman of Access Ministries, Stephen Hale, has denied breaching any guidelines, saying there have been no complaints.

"There's absolutely no evidence that week in and week out we're in any way breaching the guidelines," he told ABC Local Radio.

"There's an in-built mechanism for accountability with the Christian religious education side of things, because the lessons take place in the context of a classroom, and in the classroom is the regular class teacher.

"If what has been suggested again and again is happening, then that person, the classroom teacher, would be, one would think, suggesting that there's a problem here.

"You would have thought that if we were breaching the guidelines, there would have been a litany of complaints that would have come forward, and in fact, there haven't been any."

But Dr Cannold says chaplains' access to students extends beyond the classroom.

"The chaplain has access to children whenever, wherever and however he or she wants," she said.

Court fight

Father of six Ron Williams is challenging the National School Chaplaincy Program in the High Court.

The case, which will be heard in August, involves Scripture Union QLD and relates to a school in Toowoomba, but it is expected to have wider implications for religious organisations' agreements with the Commonwealth.

Access Ministries has called for its supporters to take "urgent action" to defend the program, which it says for some children is the "only introduction to the values that underpin a biblical understanding of God, the world, themselves and others".

Three parents have also taken a case before the Victorian Equal Opportunity and Human Rights Commission, claiming special religious education is discriminatory.

In that case, the parents allege the program segregates children on religious grounds and discriminates by forcing children to opt out rather than opting in to religious programs.

Dr Cannold says it is almost impossible for children to opt out of the school chaplain program.

"[To avoid chaplains], parents [would have to] withdraw a child from everything from school assembly to lunchtime, where the chaplain might be running a sausage sizzle, to school camp where the chaplain is very much purposely going along to pursue the aim of conversion," she said.

She says the program breaches Australia's constitution.

"Australia is not living up to the expectations of the founders of this nation, which were very much that people would be very free to practise their religion and be free to have no religion and that there ... would be religious fairness, religious tolerance, religious equality," Dr Cannold said.

"In the constitution it very clearly says there ought to be religious neutrality with regard to the state and religion, that there ought not to be a religious test for people to have jobs.

"But in order to be a chaplain, you do need to be part of a religion - indeed over 95 per cent of them are part of this very narrow brand of Christianity which sees its role in the school as missions and as trying to convert children."