A school chaplain told an anorexic student she was "hungering for the word of God", according to Greens senator Sarah Hanson-Young.

Key points: During Senate Estimates, Sarah Hanson-Young was asking Education Minister Simon Birmingham about the chaplaincy program

During Senate Estimates, Sarah Hanson-Young was asking Education Minister Simon Birmingham about the chaplaincy program She referred to a Monash University report which included the allegation about the chaplain

She referred to a Monash University report which included the allegation about the chaplain Mr Birmingham said chaplains were "not permitted to proselytise" and his department would look into it

Senator Hanson-Young used a Senate Estimates hearing to quiz department officials about the Federal Government's school chaplaincy program.

She made the allegation based on information she gathered from a Monash University report, which investigated chaplaincy services provided by Melbourne's Access Ministries.

"This university professor says that she was, quote, 'speaking to a teacher and told that the chaplain at their school, when a student went to her to talk about an issue of anorexia, said she was hungering for the word of God'," the senator told Estimates.

Senator Hanson-Young also sought a guarantee that chaplains who speak in tongues and practise exorcism for healing are not being employed in schools.

And she raised concerns about Grace Communion International, a chaplaincy provider that supports gay conversion therapy.

"This is not really the type of program or ideas, as a parent, I'd like to see being promoted to my child," she said.

"I assume I'm not the only person in room that has alarm bells ringing."

The Coalition has extended the chaplaincy program, with almost $250 million allocated in this year's budget. The program began under the Howard government in 2006.

It funds more than 3,000 schools to employ chaplains to provide pastoral care and support services.

Education Minister Simon Birmingham defended the program but said chaplains were "not permitted to proselytise".

He acknowledged the claim about the anorexic student implied "a level of proselytising may have occurred", and said his department would seek to have the "relevant jurisdiction investigate" any details.

Education Department secretary Michele Bruniges said she hoped schools would have "particular safety standards and issues in place" to deal with such matters.

The Federal Government does not have any oversight or regulation of the program. Instead, it is enforced by state and territory governments.

The peak body for chaplains wants Opposition Leader Bill Shorten to clarify whether a Labor government would axe the school chaplaincy program.

Labor has previously raised concerns about the scheme and on Thursday, Senator Doug Cameron told Senate Estimates he supports a secular school system.

"The Labor Party's position is that there should be broad-based training and it should be more professional people. That's my view," he said.

"So a secular state is what I live in and that's what I hope we continue in."

The ABC understands Labor would likely return to the model it had in government, to allow schools to employ non-religious people to provide pastoral and support services.

The National School Chaplaincy Association says the Greens are scaremongering and that complaints against chaplains are rare.