A school chaplain told a young girl with anorexia she was "hungering for the word of God", a Greens senator claims.
A Monash University professor uncovered the allegation in investigating chaplaincy services by Melbourne's Access Ministries, Sarah Hanson-Young told a Senate committee on Thursday.
She grilled Education Department officials over the delivery of chaplaincy services, which have been extended by $257 million over four years as part of this year's budget.
Senator Hanson-Young also raised concerns about Grace Communion Services, a registered chaplaincy service provider, which promotes gay conversion therapy.
"I assume I'm not the only person in the room here who has alarm bells ringing," she said.
Education Minister Simon Birmingham sought details of the anorexia incident to ensure it could be investigated by Victorian authorities.
Department secretary Michele Bruniges defended the use of services which held particular beliefs.
"I would hope from a school perspective that each of the schools would have particular safety standards and issues in place," she said.
Senator Birmingham backed the chaplaincy program as offering support for students, teachers and parents over bereavements, medical treatments, bullying, drug issues and behaviour management.
He said one student in South Australia had lost both parents, but attributed being able to get through each day to the support offered by her school's chaplain.
Chaplains are not allowed to attempt to convert students to religion, but whether chaplains could discuss the teachings of Jesus Christ depended on context, he said.