Students of faith will be "isolated" and "punished" as a result of the ACT government's incoming school chaplains ban, an opposition backbencher has claimed.
Liberal Elizabeth Kikkert made the allegation during annual report hearings on Thursday afternoon, as she grilled Education Minister Yvette Berry over the territory's decision to withdraw from the Commonwealth-funded school chaplains program.
The program allows schools to opt in for federal grants of about $20,000 a year for a chaplain.
Ms Berry has argued the faith-based role conflicts with the ACT's Education Act, which requires public schools to be secular.
She has promised existing chaplains would be offered new positions as secular youth workers from next year, although the chaplains claim they are yet to see any detail about the arrangement.
School Chaplaincy ACT has mounted a last-ditch campaign to overturn the ban, which they have described as "baffling".
At Thursday's hearing, Ms Kikkert said banning chaplains appeared at odds with the ACT government's promise to make schools inclusive and welcoming for students of all faiths and backgrounds.
Ms Kikkert asked Ms Berry if the secular youth workers would be allowed to provide students with "spiritual guidance or advice" if they sought it.
In response, Ms Berry reiterated that territory law required government schools to be secular.
"Our schools have to abide lawfully by the education act, which means that they operate in a secular way. So no, they couldn't offer religious education in that way," she said.
"That's why all religions and faiths are welcomed into our schools."
Ms Kikkert seized on that point, effectively accusing the government of discriminating against students of faith.
"It's not very welcoming at all, you're isolating those children who want to talk about spiritual issues," she said.
"It's their freedom to talk about spiritual issues at any time. You're ripping that away from them, you're stealing that away from them."
An exasperated Ms Berry attempted to interject, but Ms Kikkert pressed on.
"You are punishing them."
At the hearing, senior education directorate official Ross Hawkins confirmed the government would stump up money for schools which might struggle to pay for a secular youth worker.
The government's position on funding for the roles has shifted in the past fortnight.
Ms Berry's office initially told The Canberra Times that no new funding would be set aside to replace the $2 million that had been earmarked for chaplains in government schools through to 2022.
This week, the government said it would help smaller schools foot the bill for the roles. Mr Hawkins confirmed that position on Thursday.
"Funding already exists in [school] budgets to do this type of work and bring on ... social workers or youth workers," he said.
"But if any schools are suffering with any issues to do with funding then that will be underwritten by the directorate. No one will be short, or see funding as an issue."
Mr Hawkins said directorate staff would meet with School Chaplaincy ACT in the next fortnight to discuss the new roles.