The current buildings are no longer fit for objective.
It must ensure that "access to a full range of health services is not denied to people on the basis of the ideological or religious ethos of any healthcare provider that it chooses to partner with".
Leo Varadkar says he is sure the Health Minister will clarify who will own the property.
There will be nine people on the board of the new National Maternity Hospital - four nominated by the St Vincent's Hospital Group which is owned by the Sisters of Charity, four by the current National Maternity Hospital, including the Master, and it will be chaired by an worldwide expert in obstetrics and gynaecology.
Minister for Health Simon Harris has stood by the decision, tweeting: 'When it comes to our maternity services, I take the views of those responsible for the delivery of infants & the clinical care of women'.
It's after it emerged that full ownership of the facility would be given to the Sisters of Charity on whose land it's to be build.
"Simon Harris has wildly missed the point", she said.
Opposition parties have claimed there could be a conflict between medical decisions, the possibility of new abortion legislation, and the new owners' Catholic values.
Over 50 thousand people have signed an online petition in a bid to block the Government from handing ownership of the new National Maternity Hospital to the Sisters of Charity.
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The Sisters of Charity were party to a €128m redress scheme with the State in 2002 for child abuse, which took place at its industrial schools. "This will continue in the new hospital", said Dr Mahony.
Mr O'Riordan said the survivors group believe there should be a complete separation of Church and State, and having the religious order involved gives out the wrong impression.
"Maternity care gets to the root of how we value women in this country, and historically has been where women have been worst treated by our State", he said.
"The state is investing €300 million of your money and my money in a new maternity hospital".
"'It is correct that the land on which the new maternity hospital will be built is owned by the St. Vincent's Healthcare Group and that the Sisters of Charity are a major shareholder in the St. Vincent's Healthcare Group", reads a Department of Health statement.
The Sisters of Charity have so far failed to pay their share of funds to a redress scheme for the victims of institutional abuse.
"Well we saw what happened in the Savita Halappanavar case in Galway, and I think that issues of that kind can be posed again", he said.
"I have heard that nuns have been gifted the hospital".