This month, Education Minister Yvette Berry said religious chaplains were incompatible with the secular operation of public schools under the Education Act, and so the ACT would no longer accept federal funding for the positions. Instead, existing chaplains will be turned into youth-worker roles at the territory's expense.

But chaplains say the rules of the national chaplaincy program already forbid them from preaching their beliefs or conducting religious education, and some school communities are upset they had not been consulted.

Under the program, schools can opt in for grants of up to $20,000 a year for a chaplain, usually providing pastoral care about two days a week. Chaplains are already required to be qualified youth workers but, after controversial changes brought in by the Coalition in 2015, they must also be associated with a religious organisation.

Last year, Ms Berry wrote to the federal government requesting funding again be extended to secular workers. When the request was denied, she decided to pull public schools out of the program, though she stressed non-government schools would still be able to access the funding.

A year 12 student had collected more than 165 signatures from her peers on Friday for a letter calling on the minister to reconsider the decision, saying her own chaplain made the school a safer place and had helped her get through the stress of exams.

School Chaplaincy ACT, which employs 21 of the 22 chaplains in ACT public schools, said many schools fundraised to employ the worker for extra days on campus.

"A lot of these schools also have a youth worker or a counsellor, but they've told us they need both, or they've been unable to get a youth worker in and the chaplain's been that vital extra support person," chief executive Peter James said.

"Some people are devastated by this."

A spokeswoman for the minister said that, while the program had not received any complaints, some stakeholders had raised concerns about the non-secular nature of chaplains. Schools were not consulted prior to the ban, which has been welcomed by the Australian Education Union and the ACT's peak parents' group but has copped federal criticism.

"[We're] aware from principals that chaplains often have a valued place in their school community, which is why [they're] being offered direct government employment on a secular basis," the spokeswoman said.

Ms Berry said the territory would absorb the "the modest cost impact" of the new positions, but it is unclear how many days they will be funded to work beyond 2019. The territory has ruled out allowing chaplains to continue in public schools under community funding arrangements.

Chaplain Mandy Gray, a former social worker in the child protection sector, said donations from parents and community groups helped fund her own position on campus full-time.

"It's the best job I've ever had but I don't know what's going to happen now; they haven't told us what [the new roles] will be like," she said.

"I'm genuinely concerned for the kids."

While chaplains are banned from evangelising, they can express their own views "in good faith" when answering questions. Workers insist parental permission is still required at almost every step.

"I have one boy who always wants to chat to me but his parents have said no, so I walk him down to see his coordinator instead," Ms Gray said.

"People don't understand what we do. If I [tried to convert anyone], I'd get fired.

"But a lot of it does fall outside the typical youth worker role - I'm the [teachers'] chaplain too. Maybe someone is coping with a loss or [questioning] their purpose. I've supported staff through terminal cancer [and] abuse...I helped a Muslim student set up a prayer room, LGBTIQ students came to me to create their own support group."

But while chaplains do not have to be Christian, those employed by School Chaplaincy ACT are required to prove they can support a school community "within a Christian framework" and build relationships with churches and community groups.

A spokeswoman for the minister said such religious obligations were incompatible with public education.

"These chaplains must be active Christians who can articulate the core teachings of the Bible and its message, and from this basis do engage in discussion of religion that may not have parental consent," she said.

Ms Gray said she knew of some schools which had previously missed out on funding for a chaplain and were now concerned they would not be able to access a youth worker either.

The ACT Council of Parents' and Citizens' Associations said support workers should not be affiliated with any particular religion but stressed there was still not enough mental health professionals in schools.

The minister has hinted at more investment in youth workers and counsellors, though her office did not provide further details on Friday.

Seventy-three full-time psychologists and 31 youth workers currently work across Canberra's 88 public schools.