Despite the ruling, chaplains will remain in hundreds of the state's schools until at least the end of the year when existing funding dries up. In the interim, no government body is managing the scheme.

The federal government was previously responsible for the program, including receiving and evaluating complaints about proselytising , which is banned under the now defunct guidelines of the National School Chaplaincy Program.

Unlike the other states, NSW does not have its own policy or regulations, as chaplains were banned in its schools prior to the scheme.

Labor's education spokesman Ryan Park said it was not just about concerns of proselytism, but ensuring the government program was being implemented as intended.

“Anyone who is receiving tax-payers’ money should be required to be accountable for that and there should be some checks and balances in place to ensure that money is being spent appropriately and that we’ve got the appropriate people doing the right things,” he said.

The Commonwealth Ombudsman's 2011 investigation into the chaplaincy program found holding schools accountable to the federal department for day-to-day administration was “important in protecting the rights of parents and children affected by the program”.

The report also warned that in the absence of clearly defined protocols for both the state and federal departments “there is a serious risk that complaints will fall through the gaps”.

A spokesman for the NSW Education Department said it would investigate any claims of misconduct and refer serious allegations to the police.

But it would not be responsible for the same level of oversight as the federal government, which conducted school visits and evaluated outcomes.

A Federal Education Department spokesman said complaints should now be referred to the chaplain's employer or the school.

Peter James, a spokesman for National School Chaplaincy Association, said the lack of administration was “worth looking at” but denied there was a vacuum of regulation.

“Every chaplain has signed the code of conduct and committed to a standard and they are answerable to the employer and the school,” he said. “The fact that there’s some uncertainty about the federal layer of administration doesn’t detract from that.”

Dr Monica Thielking from Swinburne University, the national convenor of the APS Psychologists in Schools Interest Group, said it was important people working in schools came from “a highly regulated and legislated professional background”.

“It gives schools and families confidence that the people who are caring for the mental health and well being of their children are professionally trained to do so,” she said. “If it’s not regulated and there are no boundaries around the role, there’s a lot of room for error.”

“I don’t know any parent who would be happy having an unregulated person having access to their child behind closed doors to deal with their personal issues.”