The comments follow the release on Monday of a study by the Black Dog Institute, which found  its mental health awareness program was better at battling mental health stigma in schools than normal PDHPE classes.

The randomised controlled trial, published in the Journal of Adolescence, tracked year 9 and 10 students in 10 schools participating in either the institute's HeadStrong program or the standard PDHPE curriculum.

Lead author Dr Yael Perry, a clinical psychologist and researcher at the Black Dog Institute, said the results found students in the HeadStrong program had a better understanding of mental illness and were less likely to have stigmatising attitudes.

Black Dog Institute director Professor Helen Christensen said experts like herself were worried about more funding for chaplains over programs backed by scientific evidence to improve mental health outcomes.

Professor Christensen said if you wanted to treat a serious illness "would you let people choose what sort of treatment that they want, or would you choose the treatment that has the best evidence?"

The director of Monash University's mental health in schools project, Associate Professor Andrea Reupert, said while she knew of schools which had great experiences with chaplains, she, too, was concerned over government funding for the program.

"I was talking to a teacher the other day who had a student with an eating disorder and she went and saw the school chaplain who said she was hungering for the word of the Lord. I was absolutely appalled, that's not advice that was appropriate. My problem with the school chaplaincy program is that we have a trained workforce, we have a group of psychologists and welfare workers who are much better prepared to deal with the problems young people are facing than school chaplains," Dr Reupert said.

The Abbott government announced  it would be pushing ahead with a religious-only $224 million school chaplaincy scheme last Wednesday.

Announcing the scheme, Parliamentary Secretary Scott Ryan said "the government believes that school chaplains make a valuable contribution to the well-being of students and school communities".

The ACT government has said it would be demanding secular counsellors are included  as an option if  it were to administer the program, which would mean an extra $720,000 for ACT schools.

Dr Perry said having appropriately qualified staff was key to combating mental health issues in schools when one in five students  was developing depression by the time they were 18.

She said proposals for more funding for chaplains in schools was concerning.

"Once students are ready to seek help, we need to ensure that in-school support is provided by people with specialised expertise in mental health," Dr Perry said.

The Black Dog Institute delivers HeadStrong workshops for teachers funded by a $500,000 grant from the nib foundation.

The ACT also participates in the national MindMatters mental health promotion program.