Patients should be able to seek the removal of crucifixes or other religious symbols from hospital wards run by the Catholic Church, according to a Government report.
The independent review of voluntary organisations insists health services run by religious orders should be "cognisant of the impact of decor" on patients and "strive to ensure" their personal preferences are met to the "greatest extent possible".
The report also raises serious questions over whether the State should continue to fund faith-based hospital services if they refuse to provide abortions or prescribe contraceptives.
It also says there should be an onus on all organisations that refuse to provide certain services based on ethos to tell patients where they can receive such services, even if it is against their ethos.
The independent review of State-funded services also calls for a major overhaul of the structures governing charities providing health services.
The review group, chaired by former secretary-general of the European Commission Catherine Day, was asked to examine the relationship between the State and Church-run hospitals. There are currently seven voluntary hospitals owned by faith-based organisations and a further five with some degree of religious order involvement in their governance arrangements.
The 12 hospitals receive €1.34bn in State funding and are responsible for operating 26pc of publicly funded inpatient beds.
The report found there was no difference in the quality of care provided by hospitals with religious ethos and those with none.
However, some people felt religious ethos did affect the types of care provided.
A number of people who were interviewed for the report said they felt the religious ethos of an organisation was apparent in its decor, through the presence of chapels, religious icons, logos and posters.
"While not directly related to the range or delivery of services, we recommend that organisations should be cognisant of the impact of decor on patients/service users and strive to ensure that their personal preferences in this regard are met to the greatest extent possible," the report states.
In emergency situations, the report says the life and well-being of patients must always take precedence over the ethos of the religious organisation.
This means Church-run hospitals will have to ensure all legally permitted treatment is made available safely to the greatest extent possible within the capabilities available to the organisation.
Ms Day's report says the introduction of abortion raises questions over whether the State should give funding to hospitals refusing to provide the "full range of lawful services by reference to their religious ethos".
She said clarity on the constitutional rights of independently owned faith-based organisations to manage their own affairs has not yet been determined in the healthcare context by the Supreme Court.
Ms Day said it was the State's right not to fund Church-run health organisations not providing services.
But she said this would cause a "serious and prolonged disruption" to health services.
She said the decision to stop funding these health facilities was a "political rather than a legal one" due to the significant level of services provided by Catholic hospitals in Dublin, Cork and Limerick.
The report recommends the drafting of a list of essential health services which need to be provided by the voluntary or private sector or directly through the public healthcare system.
This would allow the Government move away from a provider-focused service to a system where the State commissions or buys health services it requires from organisations based on regional needs.
"This would of course not preclude any organisation, whether voluntary, public or private, from providing additional services but these would not automatically be funded by the State," Ms Day said.
She said there was currently a "breakdown in mutual trust and respect" between the HSE and voluntary organisations which "must be restored in order to maintain this essential relationship in a healthier way for the benefit of all our citizens".
The report recommends the drafting of a new charter which would help develop a "transparent and collaborative relationship" between the State and the voluntary health sector. The charter would recognise the legal status and important role played by the voluntary sector.
It also recommends the introduction of three year multi-annual budgets for voluntary organisations to allow better planning and says the levels of bureaucracy surrounding HSE compliance should be addressed.