The Federal Government has declared its ongoing commitment to funding chaplains in schools, and has flagged possible legal changes to get around a High Court decision that ruled the program invalid.

In a majority decision earlier today, the High Court decided funding for the chaplaincy program was unconstitutional because of the payment method used - not because of religious reasons.

The challenge was brought by Toowoomba man Ron Williams, who objected to what he described as a "religious missionary" being put into schools, and pointed to constitutional restrictions on any Commonwealth officers being subject to a "religious test".

While the court dismissed that aspect of the case, the ruling has a wide range of implications for how the Federal Government funds different programs.

Attorney-General Nicola Roxon says the Government has been doing "contingency planning" in the lead-up to today's ruling, and is confident it will find a way to keep chaplains in schools.

"We are committed to both the program and the funding for the school chaplaincy program...and there are different ways that we will be able to provide for the program and the funding to continue," Ms Roxon said.

"It is clear that there is a cure for each of these problems that are identified [by the court] - whether it's particular legislation, whether it's payments through the states, whether it's other sorts of contingency steps that can be taken."

If the Government decides to pursue a legislative solution to the court's decision, it is likely to have strong Coalition support.

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The National School Chaplaincy Program was set up by the Howard Government in 2006, but was later modified by Labor to allow schools to choose to employ either a chaplain or a secular student welfare worker.

Speaking shortly after the High Court handed down its ruling, Opposition Leader Tony Abbott said it would be a pity if the program was not able to continue.

"Let's look at the court's decision and let's see what the Government has in mind," he told reporters.

"We invented the program, we support the program, we want it to continue."

The Greens have long campaigned against the chaplaincy program, arguing the money should instead be spent on properly qualified counsellors for students. They now see an opportunity to overhaul how the program works.

"The Greens welcome both the overturning of the school chaplains program and the confirmation that executive government must legislate through the Parliament to a much greater extent," Greens leader Christine Milne said.

"Schools across Australia need the resources to employ properly qualified counsellors, student support officers and other non-teaching staff to help students through difficult times."

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In Queensland, many of the chaplains have been employed through Scripture Union Australia under Federal Government guidelines that state chaplains must not try to convert students to a set of religious beliefs.

The incoming CEO of Scripture Union Queensland, Peter James, is urging the Government to act swiftly to deal with the High Court's ruling.

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

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

"Chaplaincy enjoys bipartisan political support and widespread community endorsement; therefore we are confident in a speedy outcome," he said.

Federal Schools Minister Peter Garrett wants the issue resolved before the next round of payments are due later this year, and has moved to reassure those employed under the program.

"Any funding that has been received by chaplains or student welfare workers will not be withdrawn," he said.

"We are committed to maintaining the chaplaincy and student welfare program."