EMMA ALBERICI, PRESENTER: A High Court challenge to the Federal Government's school chaplains program will begin in Canberra tomorrow.

The program began under John Howard and was continued by prime ministers Rudd and Gillard.

It funded chaplains in state schools across the country.

The High Court case was launched by Ron Williams, a father of six, who claims the Commonwealth doesn't have the appropriate power to fund chaplains in schools.

John Stewart reports.

JOHN STEWART, REPORTER: Ron Williams is a father of six from the Queensland city of Toowoomba. He's a singer-songwriter by trade and an atheist who believes that religion should be kept out of state schools.

The chaplaincy program was originally introduced by John Howard in 2006.

Today, chaplains work in more than 2,000 state schools across the country.

Ron Williams says the program was a vote-buying exercise.

RON WILLIAMS, HIGH COURT LITIGANT: He might as well have said that he was going to put homoeopaths into the schools of Australia to assist the school nurse or astrologists to do readings for the children, even those capricious Capricorns or whatever. It was just absolutely ridiculous and absurd.

JOHN STEWART: The Rudd and Gillard Labor governments continued the program, and in 2012, Ron Williams won a High Court challenge.

ANNE TWOMEY, CONSTITUTIONAL LAW, SYDNEY UNIVERSITY: And he said, "Well you need parliamentary scrutiny for these sorts of things because you're spending public money," and the High Court accepted that. They said no legislation involved, there was no parliamentary legislation of it, apart from the appropriation of the money, and that wasn't sufficient.

JOHN STEWART: The Gillard Government quickly moved to create new legislation to allow the chaplaincy program to continue. Ron Williams says that over the past six years, the cost of the program has ballooned.

RON WILLIAMS: It's over, I think, $450 million, so we're heading for the half-billion-dollar mark.

JOHN STEWART: But those working as school chaplains say their work is invaluable.

ANDREA EADIE, SCHOOL CHAPLAIN: What I do is mainly a mixture of pastoral care, which is just talking one-on-one with students. It might be something as simple as a fight that they've had with a friend or it might be something that they've just discovered, like mum and dad are splitting up and, yeah, their whole life is almost been - is falling apart.

JOHN STEWART: Ron Williams says that child psychologists are better able to assist children with mental health problems. But those who train the chaplains say the program is making a difference.

PETER JAMES, SCRIPTURE UNION QUEENSLAND: Children love their chaplains and they feel comfortable talking to their chaplains. And for children who have psychological issues, the chaplain can provide almost a triage service because they are trained to recognise issues and to help the child with what can sometimes be a difficult journey of actually getting help from a psychologist.

JOHN STEWART: Professor of Constitutional Law at Sydney University Anne Twomey believes that Ron Williams could win his second High Court challenge.

ANNE TWOMEY: Oh, I should think so. I think he's got a very good chance of winning. The real question is more: how will the court deal with it?

JOHN STEWART: Last week's Commission of Audit recommended that the school chaplaincy program be abolished.

Even if Ron Williams wins his case, the Queensland Scripture Union is confident that the chaplaincy program will continue.

PETER JAMES: Whether that means continued by direct funding from the Commonwealth under the current model or whether the Commonwealth funds the states so the program continue, either way we want the program continued and we think the Commonwealth Government does too.

JOHN STEWART: But Ron Williams insists that school chaplains are a hangover from the Howard era and religion has no place in state schools.

John Stewart, Lateline.