School chaplains and religious groups have welcomed $222 million in extra funding to the National School Chaplaincy Program, but not everyone is pleased with the budget boost.

In 2007 the Howard government introduced federal funding for chaplains to work in schools, with the proviso they were not to push religion onto students.

But critics of the program say chaplains have no place in public schools, and there is evidence they are encouraging vulnerable students to join religious activities and prayer meetings.

Minister for School Education Peter Garrett says the funding will provide for the 2,700 schools that currently have a chaplain and allow up to 1,000 additional schools to access a chaplain.

"The funding will target schools in regional, remote and disadvantaged locations most in need of program support and will benefit students, parents, school staff and the broader school community," he said in a statement.

He says the voluntary program assists schools and their communities to support the spiritual wellbeing of their students.

This may include support and guidance about ethics, values, relationships, spirituality and religious issues; the provision of pastoral care; and enhancing engagement with the broader community.

Australian Christian Lobby chief Lyle Shelton welcomed the inclusion of the commitment in the budget.

"It was great to see the Treasurer Wayne Swan mention the chaplaincy funding in his budget speech," he said, thanking the Government for retaining the "faith-based nature" of the program.

Scripture Union Queensland's head, Tim Mander, also welcomed the extra funding.

"While this is confirmation of a pre-election promise, the fact that the Government has met its commitment in what is a difficult budget shows it recognises the importance of pastoral care in schools," he said.

"The exact funding arrangements haven't been finalised yet, but we hope to be able to have new chaplains on the ground in 2012."

Faith debate

But Helen Walton, the president of the Federation of Parents and Citizens in NSW, says there is evidence chaplains are proselytising in public schools.

"We are hearing anecdotal evidence from schools that... people are having prayer groups at lunchtime and actually providing a religious aspect to the sessions that they were holding with some kids," she said.

"We are definitely against that - that's not what we were told the program was about.

"We will continue to push for schools to have the right to choose someone that is going to provide the welfare they want for their school, with no faith-based aspect... and no religious aspect to any service that they provide."

Ms Walton says school counsellors are better equipped to address the issues facing students.

"What these people are working with is some of our most vulnerable young people in society - young kids, teenagers in high school who are going through some difficulties," she said.

"We'd rather have qualified people who can work with students on a range of issues including mental health.

"The chaplaincy program itself is very faith-based. Our contention was always that if you are looking at providing welfare care for students outside of the realm of a trained school counsellor role, what is needed is someone that does not necessarily have to be from a faith-based background."

David Nicholls, the president of the Atheist Foundation of Australia, agrees trained school counsellors are needed in schools, not chaplains.

"I'm not saying chaplains are nasty people, but they should not be anywhere near school children," he said.

"We need proper, accredited counsellors who have done an actual course in how to handle the problems that children face today, not people who already have ideas worked out from 2,000 years ago that are not tied into reality.

"Chaplains in state schools give credence to the idea that there is some part of the universe that we don't know about and children accept [that view]."