The group still owes €3m towards the State redress scheme
A Government minister says he is "sure" Health Minister Simon Harris will clarify ownership of the new National Maternity Hospital.
There has been widespread criticism of plans to award ownership of the hospital to the Sisters of Charity.
The group are to be the sole owner of the new hospital, as a major shareholder in the St Vincent's Healthcare Group.
In a statement, the Department of Health said: "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.
"This independence will be assured by the reserved powers which are set out in the agreement and which will be copperfastened by the golden share which will be held by the Minister for Health."
The hospital is be located on the St Vincent’s University Hospital campus in Dublin, and will cater for up to 10,000 births per year.
The build got the green light from An Bord Pleanála in March.
The Sisters of Charity were involved in five industrial schools - including St Joseph’s and St Patrick's, Kilkenny and Madonna House in Dublin.
They were party to a €128m redress scheme with the State in 2002 for child abuse which took place.
According to a December 2016 report from the Comptroller and Auditor General (C&AG), the Sisters of Charity offered €5m towards the redress scheme - but have only paid €2m.
The same report found the religious group had more than €12m in property assets around the country, which were transferred to Dublin City Council, St Vincent de Paul, the South Eastern Health Board and others as part of the 2002 deal.
The Sisters of Charity has previously issued three specific apologies relating to criminal convictions of three of its staff.
One apology in relation to Madonna House was issued in 1994, a second apology was made at the sentencing of a male childcare worker in St Joseph's in 1997 and the third apology was made when another childcare worker from St Joseph's was convicted.
The Social Protection Minister, Leo Varadkar, says he is sure Minister Harris will clarify the ownership of the hospital.
He told Newstalk Drive: "The land there is owned by the Sisters of Charity, so I guess it would have been anticipated that they would have continued to own their own land but that perhaps 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 and to merge the two boards."
"I've only seen what I've seen in the media today, and I'm sure the Minister for Health will clarify it in due course".
"I think it's important that is clarified, but like I say I'm sure Simon Harris will do that".
The Master of the National Maternity Hospital, Dr Rhona Mahony, said: "The new National Maternity Hospital to be built on the St Vincent's Healthcare campus will be dedicated solely to providing maternity care for women and infants.
"It will be operated by a new company with an independent board and will be clinically and operationally entirely independent in line with national maternity policy.
"Over 9,000 infants are born at NMH every year. The current facility is not fit for purpose.
"The co-location of this hospital with an adult tertiary hospital will revolutionise healthcare in Ireland for women and infants and we continue to work with SVHG to make a dedicated state of the art maternity hospital a reality as urgently as possible."
Several opposition parties say the move to allow the Sisters of Charity run the hospital is wrong.
Labour Party spokesperson on health, Alan Kelly, said: "Given the events of recent weeks, not to mention the failure of religious congregations to meet their share of the cost of redress, it seems extraordinary to see the State continuing to fund an increase in the asset values of those same congregations.
"The fact that the Sisters of Charity have been given sole-ownership of this land when they are party to the €128m redress scheme with the State is ludicrous.
"The Labour Party believes that into the future, all buildings that are funded by the state should be owned by the state."
Social Democrats TD Róisín Shortall said the decision was "highly inappropriate".
She said: "Why is the State building a €300m hospital with taxpayers’ money and handing it over to a religious order? It is very hard to see how there could be any rationale for this transaction.
"In addition, the fact that the Religious Sisters of Charity has failed so far to provide its share of funds to the redress scheme for victims of institutional abuse further compounds the issue as it shows a deep insensitivity towards abuse survivors."
Solidarity TD Mick Barry said the Sisters of Charity were "in serious breach of commitments given to the State regarding payments for redress for survivors of institutional abuse" and should not be "rewarded".
"The Sisters of Charity have a €3m debt outstanding on a €5m payment pledged after the publication in 2009 of the Ryan report and have yet to transfer ownership of the Sacred Heart Centre in Waterford to the State as agreed in 2002 as part of the indemnity deal.
"The Sisters of Charity refused to make any contribution to redress for survivors of those Magdalene Laundries it was responsible for."
Councillor Éilis Ryan of the Workers’ Party said: "The decision to grant ownership of the National Maternity Hospital makes a mockery of the supposed neutrality of the Citizens’ Assembly.
"Do any of us really believe that, if and when the 8th amendment of our constitution is repealed, any new legislation for abortion will be implemented fully in a hospital wholly owned by the Catholic Church?
"Every week another story emerges of the extraordinary harm done to women by the church, with State complicity, in this country. What good is it to agree, finally, to remove archaic, church-written clauses from our constitution, if we hand over women’s healthcare to that same church?".