Changes to the school chaplaincy program will rob some students of the chance to engage in faith-based discussions, an ACT religious group says.

The ACT Scripture Union has criticised the Federal Government's decision to offer student welfare officers as an alternative to chaplains from next year.

Education Minister Peter Garrett bowed to political and social pressure to change the program amid growing debate on the appropriateness of having a religious support worker in public schools.

As well as offering secular student well-being officers, Mr Garrett yesterday sought to allay community concern by introducing minimum qualifications (specifically a Certificate IV in Youth Work or its equivalent) for all those employed under the program.

He also announced minimum benchmarks for service providers, extra funding for chaplains/welfare officers in remote areas and upskilling those already employed.

A spokeswoman for Mr Garrett said it would be up to schools to source their own welfare workers from community organisations.

The scripture union's chaplaincy services director Dianne Priest said the decision was certain to reduce her organisation's role in ACT schools and she was concerned some students might be negatively affected as a result.

''My only concern is that by putting yet another secular social worker in schools, where are families and children going to go to hold faith-based conversations?'' she said.

''At the end of the day, that was whole original thrust of the program ... to provide schools and students with someone to go to talk to about spiritual matters.

''I would be loathe to see that lost from families.''

At Stromlo High School, school chaplain Ali Oliver was unfazed by the changes. She has a bachelor's degree majoring in psychology, so she already feels well-prepared for the role and said it would now be up to schools to decide which position better supported its students.

Mrs Oliver plays a key role facilitating girls' resilience programs at the high school and runs lunchtime games at Macquarie Primary School.

She has been approached about religious matters, but felt they were easily handled without the need to proselytise.

''Recently I assisted students going through Ramadan by liaising with teachers to provide a prayer room and I think that really shows what the job is all about - supporting students, staff and families regardless of their faith,'' she said.

Meanwhile, Ms Priest's comments to The Canberra Times yesterday contradicted statements she made earlier this year that the role of a chaplain was to assist students with issues such as bullying, study pressures and relationships, not give advice on matters of religion.

It also follows a highly public criticism of the program by parents and the media, with schools in other states raising concerns chaplains were proselytising, counselling students without being qualified and making homophobic comments.

ACT Council of Parents and Citizens Associations president Jane Tullis yesterday said she too was shocked by the comments after having praised the program in the past.

''I am surprised the Scripture Union has mentioned faith as the program was never established for that reason,'' she said.

''Faith-based questions, as with any other question on any other topic, are always welcome in any school and I would expect any person - teacher, administration officer, welfare officer or Christian chaplain - would be able to [answer that].''

But Ms Priest defended her comments, saying they merely reflected the fact that ''a large proportion' of Australians still identified as having Christian or other faiths and that the door needed to be kept open for ''impartial'' faith-based discussion to occur.

The Australian Education Union has labelled the changes proof that the program was ''fundamentally flawed'' and called on more funding to be invested in school counsellors and psychologists instead.

But Ms Priest said, aside from the increased choice for schools, which she respected, the new guidelines changed little. She said all 29 of her ACT chaplains were already required to obtain the minimum qualifications and that many of the new changes had in fact been proposed by the National School Chaplains Association in its submissions to federal reviews.