The High Court has ruled that the national school chaplaincy program is constitutionally invalid because it exceeds the Commonwealth's funding powers.
But Attorney General Nicola Roxon has told reporters in Canberra the government would continue funding the program, despite the landmark ruling.
In its decision, one that could cast doubt on other areas of Commonwealth funding, the court upheld a challenge to the scheme by Queensland father Ron Williams.
The Howard government introduced the scheme in 2007, offering schools up to $20,000 a year to introduce or extend chaplaincy services.
One of Australia's leading constitutional lawyers George Williams said the implications of the case were massive and could potentially affect any program directly funded by the federal government.
This would include the local government Roads Recovery program and even direct funding of private schools.
''This sets down very significant limits on the ability of the Commonwealth to spend money,'' Professor Williams said.
''I suspect this decision will embolden people to challenge Commonwealth expenditure in other areas.''
Professor Williams said that, while the Commonwealth could still provide funding, it may have to be through the states, rather than funding programs directly, which had been its preference.
''This may lead the Commonwealth to engage in a major rethink of its budgetary processes - what it spends money on and how it does that,'' he said.
"This is very likely to be the biggest High Court case of the year."
About 2700 schools have received funding under the program to date.
The Gillard government has promised to extend the scheme to up to 1000 further schools.
Professor Williams said the High Court had found the Commonwealth lacked the power to fund chaplains via executive action without accompanying legislation.
"The Commonwealth might go back and try and support the chaplaincy program with legislation but it's far from clear the High Court would uphold the chaplaincy program even with legislation," he said.
Ms Roxon said the government was committed to the program and there were different ways that it would be able to ensure funding for it.
''Governments of both persuasions of past years have relied on a very broad view of the
Commonwealth’s spending powers,'' she said.
''This decision obviously does traverse a lot of territory and we will be considering very carefully the consequences of the decision ...The direct impact is purely for the chaplains program; the indirect impact may be much more significant because this does go to the reach of executive power.''
The next round of payments for the chaplaincy program is due later this year.
Mr Williams, a father of four from Toowoomba, challenged the scheme on two grounds: that it violated religious freedom protections in the constitution, and exceeded Commonwealth funding powers.
But the High Court ruled that the case did not impact on the freedom of religion, unanimously dismissing Mr Williams's charge that school chaplains' religious position breached the constitution.
The constitution says that "no religious test shall be required as a qualification for any office or public trust under the Commonwealth" and Mr Williams had argued that the definition of school chaplains included a "religious test" for office.
But the court found that school chaplains were not Commonwealth employees, but rather were engaged by an external organisation, Scripture Union Queensland, and the Commonwealth did not enter into contractual or other arrangements with the chaplains.
But by majority the court held that the funding agreement between chaplaincy provider Scripture Union Queensland and the Commonwealth was invalid because it was beyond the executive power of the Commonwealth.
Because there is no legislation authorising the agreement, the Commonwealth argued the payments were supported by the executive power granted by section 61 of the constitution, which provides that the executive power "extends to the execution and maintenance of this constitution, and of the laws of the Commonwealth".
But the majority of the court rejected this, finding that section 61 did not empower the Commonwealth to enter into the funding agreement or make the challenged payments.
Federal Attorney-General Nicola Roxon said the government would carefully review the decision to determine if it might have wider implications.
However, she said the government was committed to maintaining funding for important community programs.
"The only government program that was challenged and invalidated by this decision was the National School Chaplaincy Program," Ms Roxon said.
"The Commonwealth has undertaken contingency planning for this decision, as we do for every High Court matter involving Commonwealth funding."
Mr Williams said he was elated by the ruling. He thanked his legal team, including solicitor Claude Bilinsky and barristers Bret Walker, SC, and Gerald Ng, and the hundreds of supporters who had made small donations to support the case.
He said he had launched the case to secure a secular education for his children.
"If we can't have a playing field within the public school system for our children that has freedom of religion and freedom from religion, I don't think there's anywhere else to go," he said.
Opposition Leader Tony Abbott told reporters in Queanbeyan that he wanted the chaplaincy program to continue but noted that he hadn't yet seen the court's decision.
"We invented the program, we support the program, we want it to continue," he said.
"Let's have a look at the decision and let's see what the government has in mind. I think it would be a real pity if this program wasn't able to continue."
"Let's have a look at the decision and let's see what the government has in mind. I think it would be a real pity if this program wasn't able to continue."
Queensland Premier Campbell Newman said he would work with the federal government to deal with any administrative issues and ensure the chaplaincy program could continue.
''I want the chamber today to know that this government is 100 per cent behind the chaplaincy program because it’s good for kids at school and it’s good for families,'' he told Queensland Parliament.
''I want the chamber today to know that this government is 100 per cent behind the chaplaincy program because it’s good for kids at school and it’s good for families,'' he told Queensland Parliament.
Scripture Union Queensland, Australia's largest employer of chaplains, which was the defendant to the High Court action, said today's decision was about a particular historical funding model.
"Even though that model might be invalid, it does not keep chaplains from supporting school communities," chief executive officer Peter James said.
"Instead, it means that a new funding model is needed."
The High Court decision that government funding of chaplaincy in Queensland schools is invalid is only "a technicality" and will not mean the end of the program, said Australian Christian Lobby head Jim Wallace.
"The government is committed to the program and I expect it will find an appropriate way of directing the funds," Brigadier Wallace said.
"There's no challenge to the religious aspect. I'd anticipate it will move quickly - we are talking about a bureaucratic solution."
Greens Leader Christine Milne welcomed the overturning of the school chaplains program.
Senator Milne said that the program's funding should go towards employing counsellors and student support staff.
"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," she said in a statement.
Senator Milne also welcomed extra scrutiny in the parliament on spending decisions.
"(We) have always believed that decisions of the executive, particularly the expenditure of money, should be subject to the scrutiny by the democratically elected parliament.''