A FATHER won the first round in his historic battle yesterday to have government-funded chaplains thrown out of the nation's public schools.

Ron Williams journeyed from Toowoomba to Sydney yesterday for a directions hearing in his challenge and was thrilled to hear that his case could be heard in the High Court over three days in May.

"This is a very important moment," a jubilant Mr Williams said yesterday.

The father of six, who has four children attending Queensland public schools, said his main argument was that the funding for chaplains in schools breached Section 116 of the Australian Constitution, which states that the "Commonwealth not legislate in respect of religion".

"This is not about getting chaplains out of schools, it's about the government funding them, which I believe is against the Constitution," he said.

If Mr Williams wins his challenge, government funding for chaplains would be removed.

The National School Chaplaincy Program was introduced in 2006 by former prime minister John Howard.

The national program won support from Prime Minister Julia Gillard, an atheist who, just before the election last year, pledged $222 million to extend the program for four years.

More than 430 schools in NSW get up to $20,000 each a year for their chaplain services, totalling almost $12 million, and more than 2500 school across Australia now have chaplains at a cost of more than $151 million.

The chaplain program is run in Queensland by that state's branch of the Scripture Union.

In NSW the program is run by the National School Chaplaincy Association which is based in Western Australia.

A spokesman for the association said yesterday it was not appropriate to comment.

NSW Greens MP John Kaye said yesterday's decision was good news for those who believed in separation of church and state. "The anger felt by many of us at the use of public money will now at least be tested in the court," he said.

"There will now be an opportunity to hear in court why this program so deeply contradicts the integrity of the Australian Constitution."

Originally published as Man 1, God 0 in school chaplains case