Speaking on RTÉ's Today with Sean O'Rourke, Mr Mulvey said he empathised with victims but the issue was separate to the one he had been dealing with. "Legal arrangements will be put in place which will 100% protect the State's investment and interest in the new hospital", said the minister.
"This new hospital must be developed in line with best global practice for maternity hospitals and be co-located with an adult acute hospital in order to ensure that women and infants have access to a full range of medical specialties".
"We need to ensure patients attending the National Maternity Hospital have immediate access to theatres, high dependency and intensive care provision in an acute adult hospital if the need arises".
Ms Mahony said means contraceptive treatment or abortions when a woman's life is at risk will be carried out at the new campus when it opens in about four or five years time.
Health Minister Simon Harris insisted during the week that the new National Maternity Hospital will have "full clinical, operational, financial and budgetary independence, free of any religious or ethnic influence".
"Can we get real about this", the leading consultant said.
18,000 people have added their names to the protest, set up after the religious order was revealed as the new owner of the facility due to be built in Dublin.
This week's controversy also meant "maternity service users have been given a strong message by the State. that the abuse they and their loved ones have suffered by religious orders do not matter", it said.
"Simon Harris has wildly missed the point", she said.
"The new National Maternity Hospital to be built on the St Vincent's Healthcare campus will be dedicated exclusively to providing maternity care for women and infants".
Almost 40,000 people have signed a petition calling on Simon Harris, the health minister, to prevent a religious order from retaining ownership of a new maternity hospital.
The group are yet to pay €3million owed to the State as part of the redress scheme following an inquiry into child abuse by the Catholic Church.
"It is also scandalous that the State will pay rent to the same group who have refused to pay their share of compensation for historical abuse that occurred under their watch".
"Especially since they still refuse to stand up and accept the consequences of this history". No private entity or religious order can profit in any way.
"And I think that we should have a situation where a maternity hospital is wholly owned and controlled by the State, and certainly not by a religious institution".
"I have heard people talk about nuns and redress".