The federal government’s school chaplaincy program has been ruled unlawful by the High Court.

The challenge to the program was the second brought by Queensland father Ron Williams, who believes there is no place in secular public schools for religious programs.

The High Court upheld his initial challenge against the program in a landmark decision in 2012 but the previous Labor government quickly passed fresh legislation to keep it going.

The court on Thursday found the Commonwealth has no executive power to fund the program.

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

Coalition government minister Kevin Andrews was the first to respond to the court’s verdict.

He said the coalition had warned Labor that 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.

The government would now need to assess how to respond to the court’s latest decision.

It’s believed more than 400 other Commonwealth programs could be affected by the decision.

The chaplaincy program was originally introduced by the Howard government in 2006 and extended by Labor.

After the decision,  The National School Chaplaincy Association (NSCA) said chaplaincy programs would still exist in Australian schools despite the High Court decision ruling their federal funding model unlawful.

The NSCA says the case is not about the validity of school chaplaincy but about the particular funding model.

“While the High Court has ruled against the current model, the court has acknowledged federal funding can continue for chaplaincy through state-territory grants,” it said in a statement on Thursday.

It hoped the federal government would act swiftly to protect the program.

However, the Queensland Council for Civil Liberties has called on Canberra to axe the program, arguing it violates the principle of separating church and state.

“In our multicultural society it is important that the state does not alienate some of its citizens by favouring one religion over the other or those who have no religion by being seen to favour religion,” the council’s president Michael Pope said, adding secular services were available to provide the type of counselling and guidance chaplains aimed to.

“Yet this is precisely what successive commonwealth governments have chosen to do by this program.”

The NSCA is addressing the media in Brisbane later on Thursday.