His comments come after after opposition parties claimed there could be a conflict of interest between medical decisions and Catholic principles.
A Government minister says he is "sure" Health Minister Simon Harris will clarify ownership of the new National 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.
He empathised with the victims but it is imperative that Holles Street would move as quickly as possible to St Vincent's campus.
"I guess it was anticipated that they would continue to own their own land but perhaps that the building would belong to the Board of Holles Street but of course the decision now has been made not to have a Board of Holles Street but to merge the two boards".
"I'm not sure exactly what the decision is there or what the plan is but I think it's important that it is clarified but I'm sure Simon Harris will do that".
Separately, he pointed out that the sisters of charity is also involved in Oasis project in Dublin's North Inner City and it receives little or no funding for this, despite treating 8,000 clients past year.
The Sisters of Charity are to take charge of the new €300m facility.
The order of nuns is among the religious congregations who owe money to the institutional abuse redress scheme.
'The new company will have clinical and operational independence in the provision of maternity, gynaecology and neonatal services, without religious, ethnic or other distinction, as well as financial and budgetary independence'.
The Religious Sisters of Charity Ireland are one of the organisations included in the Commission to Inquire into Child Abuse (known as the Ryan Commission), which unveiled a vast amount of systematic institutional abuse going back decades.
Workers' Party councillor Éilis Ryan also strongly criticised the move.
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