Katie Pratt spends 22 hours a week working as a chaplain at a primary school in Canberra.

"I love coming alongside people and being a support for them," she said.

"I love hearing about their stories. I love walking beside them while they're going through the wins of life, and going through the challenges as well."

But as of next year, Mrs Pratt, who is a trained counsellor and holds a community education degree, will go from being a frequent figure at her school, to being there 10 hours per week — and it is unclear how any gaps in support for students will be filled.

The ACT Education Directorate is opting out of the National School Chaplaincy Program in 2020, in a bid to "take the religion out" of public schools.

Costs currently met by the Commonwealth under the program will be picked up by the ACT Government, but the additional hours many chaplains work, funded by Scripture Union, will be lost.

"Federal funding allowed us 10 hours and the ACT Government is going to match that, but they have not been aware that we have community funding as well," Mrs Pratt explained.

"So, I'm doing an extra 12 hours on top of those [government-funded] hours.

"Those extra hours will be lost in this new role, because that community funding and those partnerships won't be allowed in this new space."

Concerns over how new role will meet students' needs

Some parents are concerned about the way the reduction in hours will affect their school. ( ABC News: Tim Swanston )

In 2020, chaplain positions will be rebranded as "school wellbeing officers" and staff given 10 hours of work per week.

"They have a period by the end of this week to decide whether that role will be suitable for them," ACT School Chaplaincy chief executive Peter James said.

"Recognising that it's fewer hours than they've been working so far [because] it's an entirely government-employed role now, so the capacity for the community to invest in the role has been removed."

Chaplains in the schools that have opted in to the current program hold concerns about how they are going to meet students' needs under the new job plan.

"I'm not sure how I'm going to do the new role in 10 hours, when being there and building relationships with people takes time and you just need to be there on the ground," Mrs Pratt said.

"I am worried that I won't be able to be a full support to students because I'm just not going to be in the school enough.

"It will be a hit to some chaplains who won't have the full-time work they need, but we're more grieved over the loss for the students — that they won't be receiving that support."

Concerning the loss of the Scripture Union-funded hours, a spokeswoman for Education Minister Yvette Berry said:

"In a situation where an existing chaplain was funded separately for additional hours, the principal will manage this staffing change like any other and undertake their usual process of assessing the needs of their school community and allocating staffing resources accordingly."

The spokeswoman also noted that "all ACT public schools have access to psychologists, social workers, speech pathologists, occupational therapists and specialist educators".

"In addition, in 2016, ACT Labor committed to 20 additional school psychologists which are now funded as part of the 2019-20 Budget," she said.

But chaplains, who are all required to have the national standard Certificate 4 in youth work or community work, see their position as complimentary to these support staff.

"Kids are not always comfortable with going to a psychologist to get the support they need, and then the psychologists are flat out in our schools," Mrs Pratt said.

"The teachers and psychologists want to care for the students but they just don't have that extra time that they need, whereas the chaplain can be there and available.

Parents ask government to 'please rethink this'

Amanda Howard has two children at a local public school in Canberra. ( ABC News: Tahlia Roy )

The situation concerns parents like Amanda Howard, whose children attend one of the 22 public schools in the ACT that use the current program.

She saw the chaplaincy program in action when a kindergarten teacher at their school was diagnosed with a terminal illness late last year.

"She entered into palliative care, which of course is very hard for kids who are in kindy, and very hard for the other staff members at the school," Mrs Howard said.

"The chaplain visited her in the hospice, looked after her and her family, and set up a meals roster among the kindy mums.

"When the teacher passed away earlier this year, this chaplain not only counselled and grieved with these other staff members, and with students who were very upset, but also then helped to organise her funeral, helped to cater for her funeral, helped staff members to get to the funeral, and has followed up with that family since.

"I can't tell you how important that has been for our school community and how important that has been for us as a school to be able to help in a really practical way. I'm very sad to think that she might have to go in the future."

Similarly, a petition set up by the Malkara Parents and Citizens Committee asks the ACT Government to "please rethink this".

"Our beloved chaplain, Reverend Andrea de Vaal Horciu [is] a woman who has devoted her life to helping families with children with disability," the petition states.

"She works with all of our families: atheists, Muslims, agnostics, Christians and everyone in between. No other youth worker will do anything but the set hours.

"Try explaining that to my eldest son, or to the refugee girl with cerebral palsy whom Andrea has sustained for three years.

"Please don't take away our choice. We wholeheartedly support the right of other schools to choose. We respect and need our chaplain."

Why the ACT are withdrawing from the Program

ACT Education Minister Yvette Berry said religious workers were "incompatible with the education act". ( ABC News: James Fettes )

When the ACT Government first announced their plan to end affiliation with the National School Chaplaincy Program in February this year, 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 at the time.

Ms Berry's spokeswoman yesterday reiterated the government's stance that religious chaplains are inconsistent with secular education:

"Public schools are required under the Education Act 2004 (ACT) to operate in a secular, non-sectarian way, and religious chaplains are incompatible with this objective. "The decision was made to uphold the requirements of the Act. The ACT Principals Association, the ACT Council of Parents & Citizens Association and the Australian Education Union support the decision."

But Mr James said the government had interpreted the Education Act incorrectly, and had dismissed the desire schools who currently participated in the program had for spiritual input.

"Secular education means that students get to learn about the practical things that will equip them for employment and life beyond school. That's a good thing, and it's been enshrined in legislation since the 1880s," he said.

"Secularism was never meant to exclude the opportunity for a child to explore what they believe, as part of their world view formation.

"We live in a multicultural society, we have people who come from rich cultural heritages that include beliefs, and sometimes beliefs that are inseparable from those cultural heritages."

Mr James said most people dealt with life's questions with some sense of spirituality.

"They may not have a particular religion that they wrap around that, and that's fine, but what we say is that secularism should be inclusive, it should be a principle that preserves the right of every child and young person to explore belief and express belief as they see fit, and including the right to decide that they don't believe," he said.

"This decision would exclude the right of children to be supported in schools about spiritual beliefs."

Religious chaplains will be replaced by welfare workers from next year. ( ABC News: David Lewis )

Mrs Pratt said chaplains were given strict instructions around proselytizing and sharing their faith.

"We had very clear guidelines under School Chaplaincy ACT about how we could talk to students [spiritually]. It would only be if students and families initiated conversations with us of a spiritual nature," she said.

"Currently, us 'chappies' are able to be available to everyone in the community regardless of faith or worldview.

"If someone does come to us with a spiritual question or thought, they can share that with us and we can talk openly about that with them.

"But otherwise, we're there as a social, emotional and spiritual support."

Mr James added that school chaplains had been operating in Canberra schools for 26 years, and "there's not been a single complaint about inappropriate spiritual conversations or proselytizing".

"It's a voluntary program, schools don't have to have a chaplain, and it's also voluntary in the sense that students and parents get to choose whether they want their son or daughter to have any connection with a chaplain," he said.

"It's a program that, when you talk people in schools that have chosen it, it is outstandingly successful."

While the chaplaincy association is disappointed the changes are being pushed through, the ACT Government says it remains committed to "the wellbeing of all ACT school students, which is an important part of enabling access to learning, and already invests significantly in school supports through qualified psychologists, youth workers and other support staff".

They also stated that "non-government schools in the ACT should be able to continue to access the federal funding available through this program".