In February, the ACT became the first jurisdiction to pull out of the Commonwealth-funded chaplaincy program, saying the role conflicted with the secular operation of public schools required under the ACT's own education act.

The national scheme allows schools to opt in for grants of $20,000 a year for a chaplain, supporting students two days a week, with extra hours often funded by the community.

While chaplains must already be qualified youth workers, the ACT government has been at odds with the Coalition since it brought in controversial changes requiring they also have ties to a religious group. Chaplains are banned from preaching or teaching religious education but can offer spiritual support with parental permission.

ACT Education Minister Yvette Berry has promised to offer all existing chaplains the same 10 hours of funding but as secular youth workers in the public service.

Just weeks out from the end of the school year, chaplains say they are still in limbo, yet to see any detail about the new roles starting in February.

Earlier this month, Ms Berry's office told The Canberra Times no new money would be set aside to replace the close to $2 million from federal coffers that had been earmarked for chaplains in ACT public schools until 2022.

Instead, schools themselves would foot the bill for the roles, though the education directorate would pitch in for small schools in need.

On Wednesday, a spokeswoman further clarified that the government would give funding to those who couldn't afford to replace their chaplain and stressed no money would be drawn out of parents' groups.

Schools were well-resourced, she said, and could make their own decisions on staffing but the "modest cost" of a chaplain equal to the hours funded by the national program was considered within their existing means.

Yet, weeks before Bruce McCourt retired in July as principal of a large public high school, he was crunching the numbers to keep his own chaplain on and coming up short.

"I was told [by the directorate then] no new money would be coming, but I didn't have any to spare and I didn't want to cut any of my other well-being staff," he said.

"Most schools are in the same situation."

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Schools weren't consulted prior to the ban, which has since been backed by the public sector's teachers' union and principals' association.

While the ACT's peak parents' group agreed chaplains should not have to be religious, they were "extremely disappointed" to learn the money to replace them was coming out of already-stretched school budgets when more support workers were "critically needed".

The union has agreed schools need more support staff, a key recommendation of a recent inquiry into school violence, but warned the chaplaincy program was designed by the Coalition's "zealots" to force Christianity into secular schools.

On the ground, Mr McCourt said the minister's decision came as a shock, even, it seemed, to the directorate itself.

"This was a free program in schools, chaplains were there to listen or run art classes and breakfasts, they weren't trying to convert anyone," Mr McCourt said.

"To take Commonwealth money out of the education system like this is quite extraordinary. The government doesn't seem to understand what chaplains do."

He called on government ministers to spend a day in a school with a chaplain to "see what it's really like".

While chaplains do not have to be Christian, Canberra's peak employer School Chaplaincy ACT requires all employees to demonstrate "a living relationship with Christ" and build relationships with churches.

Mr McCourt said his own chaplain had brought in members from her church to run extracurricular activities - but in music not religion.

"I've never had any concerns or complaints," he said.

"At every school I've had a chaplain, they've made such a huge difference not just for the students and families but for staff as well. They're a safe person to talk to. Our chaplain even officiated two staff weddings."

School Chaplaincy ACT said there hadn't been any complaints about the program in its 26 years in the ACT and it was only aware of one school out of the 22 affected which had been offered extra government funding to replace their chaplain so far.

On Wednesday, the government said no chaplains had yet turned down the offer to stay on in secular positions and flagged a meeting would be held with affected workers at the end of the month.

Mandy Gray is a former social worker who now works full-time as a public school chaplain thanks to donations.

"I'm desperate to stay, but we haven't heard anything from the government and my principal is trying to find the cash, either way my hours will have to go down," she said.

"I get kids and staff every day coming to my office to ask me if I can stay, I don't know what to tell them."

School Chaplaincy ACT estimates as many as 900 support days could be lost under the ban in Canberra schools, as most chaplains on average work 15 to 16 hours each week thanks to community donations. The government has already ruled out allowing chaplains to continue on under such fundraising arrangements.

Dozens of students have since called on the ban to be reversed as part of a campaign funded by School Chaplaincy ACT. In response to growing backlash, ACT Labor has since launched its own petition calling on people to support the decision.

While some students who spoke to The Canberra Times said they didn't know their chaplain very well, many have credited them with keeping them in school and, in a number of cases, managing serious challenges like anxiety and grief.

The federal government has also lashed the ban, accusing Ms Berry of "putting ideology above student welfare".

But in 2014 its own decision to cut off funding to secular chaplains was done without consultation, affecting 14 ACT schools, and leading to a discrimination challenge in a Victorian tribunal.

Writing in The Canberra Times this week, Australian Education Union ACT secretary Glenn Fowler warned of the dangers of a national chaplaincy program with religious requirements.

"It is not as problematic as Fred Nile's scripture classes in [NSW] public schools, but it is problematic," he wrote.

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