National School Chaplaincy Association secretary Peter James has also advocated the benefits that religious chaplains can bring over secular student welfare workers, as thousands of schools await federal government moves to provide funding for the program through a new route.

''I think the government announcement [in the budget for $245.3 million until the end of 2018] was for chaplaincy only, and the way they explained that was to change the program to its original core and intent,'' Mr James said.

''It was a 20 per cent cut in funding [for] next year … and I don’t see them funding an alternative [to chaplains].

''The states and territories can fund the alternative if they want to; there’s no questions about the choice, it’s a question of who funds it.''

Mr James – who is also the chief executive of Scripture Union Queensland, which manages chaplains in the ACT – said chaplains, who require parental consent before meeting with students, came with the same skills as a social worker but were also able to answer questions of faith when the child asks them.

''The child has to raise it and the way the response has to be crafted is a non-manipulative, non-coercive response,'' he said.

Asked how a Christian chaplain could provide spiritual guidance to a Muslim student, the former lawyer said the position was to be supportive, not to provide a counterpoint.

''The chaplain might say, 'What does your family believe about that? Do you have someone who can help answer that?' ''

ACT Education Minister Joy Burch has said she will work with her federal counterpart, Christopher Pyne, to ensure money continues to flow, but believes ACT schools should be able to choose between funding for a religious chaplain or a secular student welfare worker, as has occurred under federal arrangements during the past 18 months.

Just under half of all ACT schools – 56 of 130 – employed a federally funded chaplain (31) or secular welfare worker (25) this year.

There was no response from Mr Pyne to questions this week.