PM Tony Abbott says the government will closely study the High Court's decision to declare the chaplaincy program invalid.

THE High Court has ruled against federal government funding of school chaplains.

Today it upheld the objections of Queensland father Ron Williams, who launched the case arguing there was no place in public schools for non-secular programs.

Former prime minister John Howard introduced the controversial program in the lead-up to the 2007 election. It allows Australian schools to apply for $20,000 grants towards the cost of employing a school chaplain.

Mr Williams, a Toowoomba father-of-six has self-funded two cases against the program with the help of donations from other parents.

“Public schools aren’t a place for religious missionaries, with or without government funding. The fact the federal government was funding them was adding insult to injury,’’ Mr Williams has previously told The Australian.

Mr Williams said his aim in launching the latest round of litigation was to “keep the bastards honest” by ensuring all Commonwealth spending was properly scrutinised by parliament and the public.

His first legal action was also upheld by the High Court but the Gillard government rushed through emergency legislation to keep the program going.

The current government also seems to be considering legislation but has not made a decision on this yet.

School chaplains will not be leaving schools immediately. The Scripture Union (SU) Qld chief executive Peter James said today that existing funding would allow the program to continue until the end of this year.

Mr James said the program had bipartisan support and he felt confident that some type of funding, which could ultimately come from state rather than federal government, would also see it continue.

“We are confident some form of funding will be put in place,” Mr James said.

During a press conference this morning Prime Minister Tony Abbott said the government would carefully study the judgment and make an appropriate response.

He said the government supported the program and wanted it to continue.

Social Services Minister Kevin Andrews told SkyNews that the government was neither disappointed nor pleased with the decision.

“It has been a very valuable program but obviously we’ve got to make sure that any legislation for a program meets the constitutional requirements,” he said.

Mr Andrews said the government is yet to decide if it will attempt to rewrite the legislation so that the program can continue.

But he said the coalition had warned Labor its legislation responding to the court’s first ruling wouldn’t stand up, and that view appeared to have been vindicated.

“The previous government didn’t get it right,” Mr Andrews told Sky News, referring to legislation Labor introduced in 2012 after Mr Williams’ first victory.

In a sign of bipartisanship, Labor has called on the government to take the necessary action to make sure programs can continue in the wake of the court’s decision.

“Australians are still reeling from the Government’s unfair budget and Tony Abbott should not use today’s decision as an excuse to cut deeper,” Shadow Finance Minister Tony Burke said in a statement.

“Tony Abbott needs to make clear to the Australian people that he will continue to support funding for important Commonwealth programs that may be affected by the High Court’s decision.

“Given the potential far-reaching effect of this judgment, Labor is prepared to offer bipartisan support on this issue to ensure the continuity of Commonwealth Government programs.”

Mr Burke said amendments made in light of the 2012 landmark judgment were an “interim measure” and were also bipartisan.

In 2012 the High Court ruled funding for the chaplaincy scheme was invalid because it was not supported by specific legislation passed by parliament.

Within days the Gillard Government had pushed through legislation but the High Court today found this was invalid because the legislation was not supported by a specific head of constitutional power.

Funding for more than 400 other government programs covered by the legislation is also in doubt because of the decision, including the National Disability Insurance Scheme, local infrastructure schemes, funding for surf clubs, drought assistance, counter-terrorism funding and job services.

The government has allocated $243.8 million in the Budget for the chaplain program over the next four years.

Following the Budget announcement, Education Minister Christopher Pyne said an alternative option - introduced by the previous Labor government - which allowed schools to appoint a non-religious student welfare worker instead of a chaplain, would be removed.

In its judgment, the court found that the program was unlawful and that the Commonwealth had no executive power to fund it.

“The making of the payments was therefore held to be unlawful,” the court said in a unanimous summary judgment.

The National School Chaplaincy Association (NSCA) has released a statement saying the High Court case is not about the validity of the school chaplaincy program, but the federal model it is funded by.

“While the High Court has ruled against the current model, the court has acknowledged federal funding can continue for chaplaincy through state/territory grants,” the statement says.

“ In 2012, the High Court ruled unanimously that, funding model aside, there is no constitutional problem with chaplains serving in government schools.

“Therefore we hope the Federal Government will again act swiftly to protect this vital and beneficial program for students.”

Ahead of the result Coalition MP Andrew Laming, who helped start the program, slammed the action as “frivolous”.

“I look directly in the eyes of the loose alliance of Greens, gays and atheists who have mounted this continuous campaign against chaplaincy: you are clearly out of touch,” he told reporters this morning.

“We’ll legislate regardless of the decision today to ensure that important programs like chaplaincy can occur.”

The school chaplains program has been criticised for harming gay and lesbian children with outgoing Labor Senator Louise Pratt saying a survey had found anti-gay chaplains had driven schoolchildren to self-harm.

Twitter reaction was swift, with most supportive of the decision.

YESSSSSSSSSS RT @abcnews: #BREAKING School chaplaincy funding struck down in High Court http://t.co/EnczrLzd89 — Shelley Stocken (@shellity) June 19, 2014 Sub-type: comment CAPTION: YESSSSSSSSSS RT @abcnews: #BREAKING School chaplaincy funding struck down in High Court http://t.co/EnczrLzd89— Shelley Stocken (@shellity) June 19, 2014 Sub-type: comment CAPTION: YESSSSSSSSSS RT @abcnews: #BREAKING School chaplaincy funding struck down in High Court http://t.co/EnczrLzd89— Shelley Stocken (@shellity) June 19, 2014

GOOOOOAALLLL RT @abcnews: #BREAKING High Court rules in favour of a challenge to Commonwealth funding of school chaplains #auspol — Snoop Evangelion (@methadonna) June 19, 2014 Sub-type: comment CAPTION: GOOOOOAALLLL RT @abcnews: #BREAKING High Court rules in favour of a challenge to Commonwealth funding of school chaplains #auspol— Snoop Evangelion (@methadonna) June 19, 2014 Sub-type: comment CAPTION: GOOOOOAALLLL RT @abcnews: #BREAKING High Court rules in favour of a challenge to Commonwealth funding of school chaplains #auspol— Snoop Evangelion (@methadonna) June 19, 2014