The Taoiseach has said that the ethos of a publicly funded hospital should reflect the public as a whole and not just one religion.
It is after a new report recommends that hospitals run by religious orders should remove Catholic statues and crucifixes if a patient asks.
The independent report also found that there was no difference in the quality of care by hospitals with religious ethos and those with none.
There are 12 hospitals around the country that are either owned by faith-based organisations or have some degree of religious order involvement.
Taoiseach Leo Varadkar said times have changed.
"Charities and religious bodies that run hospitals and such should have regard for the fact that in modern Ireland there's now diversity of views on religion and so on.
"It is the 21st century; a lot of patients, a lot of kids aren't religious, maybe aren't Roman Catholic and the ethos of a publicly funded institution should reflect the public."
Earlier: Church-run hospitals are being told to remove crucifixes if a patient asks.
A new Government report has examined the relationship between the State and hospitals run by religious orders.
It has told the hospitals that they should be conscious of the impact that decor can have on a patient.
The review concluded that the life and well-being of patients must take precedence over religious ethos.
Political commentator John McGuirk says he doubts many patients are worried about religious symbols on display.
He said: "If you are in a hospital and you're sick I think the last thing you're worried about is what's on the wall.
"I think you're much more worried about what the doctors are doing or whether they are capable of treating you.
"I also think that in many hospitals, particularly where people are very very sick, the fact that they are religious in nature and they have a chaplaincy and often times they have more than chapels, is a vital part of what they do."