Non-Christian chaplains are accusing Calvary Public Hospital Bruce of denying them easy access to patients of non-Christian faiths.
The spiritual counsellors say they are integrated into the system at Canberra Hospital, which is run by the ACT government.
But they say they are kept on the outside of the system at the Catholic-run institution.
Chaplains offer "pastoral care" which may be specifically religious or just the simple holding of a hand. Many of them are priests but other religions have their own chaplains.
The Muslim hospital chaplain in Canberra said he had asked Calvary for better access to Muslim patients but had been rebuffed.
"This is not good enough. I am sure other faiths would have their chaplain visit them," Hashim Abdul Rahman said. "I'm not happy."
He said the Catholic hospital would only call him if a patient specifically requested a Muslim chaplain. But he said he was not allowed to know who the Muslim patients were, as he was at the ACT government's Canberra Hospital.
He said he had been called by Calvary to help a patient only three or four times in five years. He had organised Muslim funerals when a patient died there but, in his opinion, that wasn't good enough: "I need to see patients before they die but I can't unless the family call," Mr Hashim said.
In contrast, Canberra Hospital has a list of the names of patients who have consented to disclose their religion.
The list is updated frequently so that chaplains of all faiths know whom they might visit. Mr Hashim scrutinises the list and then goes to the ward to see if he can help with the patient's spiritual and emotional needs.
He had raised the matter of access with Calvary. "I said I would like similar access as I get from Canberra Hospital," he said.
Calvary responded that no names and religions could be disclosed as a matter of privacy, the Muslim chaplain said.
Humanist chaplains (who do not believe in any god) say that Calvary has erected unnecessary barriers when they have tried to get access to the Catholic hospital.
"At Canberra Hospital, since 1995, we humanist chaplains have been officially administering to the increasing number of staff, patients and their families who are un-churched, non-theist," Charles Foley said.
"However, the Calvary Hospital Catholic-dominated chaplaincy refused to allow each of us to serve at their hospital and hospice as members of their chaplaincy staff. We fully expect that to change after the takeover."
Calvary denied there was any discrimination.
"In line with our values, we deliver pastoral care, by providing spiritual and emotional support to all people according to their need when attending Calvary Public Hospital Bruce," Mary Ringstad, Calvary National Manager Pastoral Care, said.
"We do not restrict or prevent anyone accessing the support of pastoral care while they are a patient at Calvary Public Hospital Bruce, rather adopting a model that provides flexible, adaptable and contemporary support to those who are feeling vulnerable while in hospital."
