A QUEENSLAND dad has won an historic court case that has overruled federal government funding for chaplains in schools.

In a case described as an attempt to "sue God", Toowoomba father Ronald Williams argued the school chaplaincy program was unconstitutional.

Mr Williams objected to the chaplaincy program at his children's school, Toowoomba's Darling Heights State School.

After a long-running legal battle, the High Court this morning backed Mr Williams' claims that the program is invalid under the Constitution.

The case could have huge implications for federal funding of other programs and organisations, including councils.

The majority of the court also ruled that payments the Commonwealth made to Scripture Union Queensland were not supported by section 61 of the constitution, which defines executive power.

Section 61 says the Commonwealth's executive power "extends to the execution and maintenance of this constitution and of the laws of the Commonwealth".

The court ruled that this did not empower the federal government to enter the funding agreement to make the payments.

In particular, it said the power did not include the parliament authorising the executive, or ministers, to enter agreements or contracts, a summary of the judgement said.

As well as arguing payments for the program were invalid, Mr Williams also challenged it on the grounds of the constitution banning religious tests for Commonwealth officers.

The court unanimously dismissed that part of the challenge, saying chaplains employed by Scripture Union Queensland did not hold office under the Commonwealth.

Attorney General Nicola Roxon said the government was considering whether it needed to change funding for other programs.

"The Government is committed to maintaining funding for important community programs," Ms Roxon said in a statement.

"The Government is carefully reviewing the reasoning of the High Court to determine what, if any, wider implications the decision may hold."

Responding to the High Court decision, a peak chaplaincy group said the funding issue was a relatively minor glitch that could soon be remedied.

Queensland's largest employing authority for school chaplains, Scripture Union Queensland, asked the Federal Government to act quickly to ensure funding remained protected.

Incoming CEO Peter James said the High Court finding was in favour of chaplains continuing to operate in Australian schools.

The funding decision was unwelcome, but could be remedied, he said.

"This decision means that for the vital work of chaplains to continue we need a new funding model," he said.

"We will be working with the Federal Government to ensure that happens."

Mr James said over 2000 school communities across Australia had chaplains and many would lose their chaplain if the new federal model was not put in place.

"Chaplaincy enjoys bipartisan political support and widespread community endorsement, therefore we are confident of a speedy outcome."

Originally published as School chaplaincy funding ruled 'invalid'