Health Minister Simon Harris says the Sisters of Charity will receive no financial gain from the new National Maternity Hospital.
There have been protests and objections to putting the new facility into the ownership of the religious order.
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.
A report from the Comptroller and Auditor General (C&AG) in December 2016 shows that the Sisters of Charity offered €5m towards the redress scheme - but have only paid €2m.
An online petition against the ownership has received more than 65,000 signatures.
There are also calls for a Dáil debate on the issue.
On Newstalk Drive, Minister Harris said the Government will not proceed with the project unless the Department of Health is satisfied that the hospital will be free of religious interference and that the state's investment will be 100% protected:
“From my perspective and from my perspective I want to make sure of two things," he said.
"One, that no religious order profits in any way from this - this is a public facility and I want to make sure that the state’s investment is 100% protected.
“And secondly, I want to absolutely make sure that contracts, licences and legal agreements – which have yet to be drawn up remember - will entirely protect the clinical, operational, budgetary and financial independence.”
Meeting with HSE Director-General
In a statement earlier, Minister Harris said: "The State’s financial and public health interest in this hospital must be fully protected. No private entity or religious order can profit in any way.
"The building can only be used for the defined purpose of providing public maternity, gynaecological and neonatal services.
"Robust contractual arrangements must be put in place to make sure that this is a reality."
Mr Harris said he has met the Director-General of the Health Service Executive (HSE) Tony O'Brien - and has requested that before any contracts are entered into, these three criteria must be fully satisfied.
"In all such cases, where the HSE undertake capital development, legal mechanisms are put in place to ensure that the State's investment is protected and that the facilities are secured for the continued use of public patients.
"This must and will be the case in relation to the new Maternity Hospital."
On the question of finances, Minister Harris said: "The St Vincent's Healthcare Group is making available very valuable land at no cost to the State, to facilitate the relocation of the National Maternity Hospital.
"In doing so, they have foregone the opportunity to put this land to alternative use.
"Let me very clear: there will be no financial gain to any religious order from the development of this hospital.
"Legal arrangements will be put in place which will 100% protect the State’s investment and interest in the new hospital."
'Nuns will not run the hospital'
On the running of the facility, Minister Harris explained: "I have heard people say that nuns will be running the hospital. Not true.
"I have heard that nuns have been gifted the hospital. Not true. I have heard people talk about nuns and redress.
"Redress is extremely important and I have previously said that the religious orders must step up to the mark and pay what is long overdue.
"However, I think it is wrong to conflate redress with the decision to build the desperately needed new maternity hospital."
Plans to relocate the National Maternity Hospital to St Vincent’s were announced in May 2013.
The site is owned by the St Vincent's Healthcare Group, of which the Sisters of Charity are a major shareholder.