Chaplains will be banned from Canberra's public schools from the end of the year in a move that goes beyond federal Labor policy to allow a choice of religious or secular workers.

Key points: No more chaplains will be allowed to work in Canberra public schools from next year

No more chaplains will be allowed to work in Canberra public schools from next year Those currently employed will be forced to work in a secular capacity

Those currently employed will be forced to work in a secular capacity The ACT's chaplain community has condemned the move

The School Chaplaincy community has slammed the decision, saying it is "removing choice from parents", and it is "ludicrous" to keep current chaplains on in non-religious roles.

The ACT's Education Minister, Yvette Berry, said on Friday there would be "no more chaplains in ACT government schools" after a decision to end the National School Chaplaincy Program in public schools after 2019.

Currently, the territory's schools can voluntarily opt in to the federal program, which provides up to $20,000 in funding for chaplains.

However, under the Coalition Government the workers must have a religious affiliation.

Ms Berry said the ACT education act mandated that the territory's public education sector was secular.

"All we're doing is taking the religion out of it," she said.

Chaplains currently employed in about 20 ACT schools will be allowed to stay on but they will have no authority to teach religion.

"They're employed to continue to do that youth work and social work, which is important," Ms Berry said.

"But that is conducted in non-religious way."

Public schools will not get to choose if they want to employ chaplains in the ACT. ( ABC News )

Federal Labor this week confirmed it would allow schools to choose whether funding went to chaplains or secular workers if it won the next election.

Repeatedly asked if territory schools would be able to decide whether they wanted a chaplain or a secular worker under that policy, Ms Berry said religious workers were "incompatible with the education act".

"There will be no more chaplains in ACT government schools," she said.

The decision comes after the ACT Government wrote to the Federal Government requesting the chaplaincy funding be extended to secular workers.

That request was denied.

Chaplains say decision removes choice from parents

School Chaplaincy ACT chief executive Peter James said the decision removed parents' choice in the matter and could impact the wellbeing of students in the territory.

"These school communities love their chaplains, they've chosen to have their chaplains voluntarily," he said.

"Our concern is schools will be denied that support."

He described the plan to continue the employment of chaplains in secular roles as ludicrous.

"They wouldn't be there to listen and engage with students about spiritual issues," he said.

"So in a time of grief and loss, or a student who has a faith background that they want to engage with and explore with a person who's trained in that space, that just wouldn't exist anymore in Canberra schools."

He said spirituality was a requirement of high-quality education.

"It seems that, at least in government schooling, [Ms Berry] doesn't seem to think that students and parents should be allowed to have that choice," he said.

ACT Education Minister Yvette Berry has taken a stronger stance on the matter than the Chief Minister. ( ABC News: Elise Pianegonda )

Chief Minister at odds with deputy over 'culture war'

Despite Ms Berry's hard-line stance, Chief Minister Andrew Barr appeared to be satisfied with federal Labor's policy.

"Clearly if there is a change of [federal] government we're going to have that flexibility in the program nationwide, and from my perspective I think that's a good thing," he said.

He said it was the impost of religion that was problematic.

"If school communities wish to continue those arrangements that's fine, I have no problem with that, but it shouldn't be forced upon schools and there should be flexibility," he said.

"Chaplains can add value but you shouldn't have a religious focus forced upon a school.

"This is a culture war being played out in our schools and it is not appropriate and we think there is a better way."

If Labor does not win the next federal election, the ACT Government would have to absorb the cost of continuing to employ current chaplains in secular roles.

Ms Berry said the transition would come at a "very minimal cost" to the ACT.

Non-government schools can continue to participate in the national program.