Cardinal Sean Brady has said that enforcing the proposed abortion legislation across all hospitals could lead to potential legal action against the reforms.
“We believe that is a denial of fundamental religious freedom,” he said.
“It’s not just hospitals, it’s schools. This is very potentially menacing for institutions and for the expression of religious thought in this country.”
The Catholic bishops had earlier branded the proposed changes to Ireland’s strict abortion regime as dramatic and morally unacceptable.
The church hierarchy said the deliberate decision to deprive a human being of life is always morally wrong.
The Bill was published late on Tuesday night after intense discussions between the coalition parties Fine Gael and Labour.
Cardinal Sean Brady said the bishops have not discussed whether politicians who advocate support for the legislation should be barred from communion, as has happened in some US dioceses.
“There would be a great reluctance to politicise the Eucharist,” he told RTE Radio.
“I say that they (politicians) have an obligation to oppose the laws that are attacking something so fundamental as the right to life and they would have to follow their own conscience.”
Tánaiste Eamon Gilmore said the Government has a duty to bring in the abortion law.
“They (bishops) are entitled to express their point of view. This is a democratic country,” the Labour leader said.
“But it is time that that legislation was dealt with.”
Mr Gilmore said it was reasonable for individual healthcare professionals to have conscientious objection to abortion.
“But what we have to do collectively as a society and legislators is make laws that make it clear what is the position for a pregnant woman whose life is at risk, what treatment is available to her,” he said.
“She needs to be assured that her life will be saved, that she will not be at risk of death and that the medical professionals who treat her know exactly where they stand if they act to save her life. That’s our duty as legislators.”