Its clinical director, Professor Mary Wingfield, has brushed aside fears that treatments like IVF won't be allowed there due to its ownership by a religious order.
Instead she argued that the move by the Merrion Fertility Clinic will "benefit our patients".
The clinic - where NMH master Rhona Mahony is a voluntary director - is currently based on Lower Mount Street, and pays rent to the NMH next door.
It provides services like IVF to couples who are having difficulty conceiving - both public and private patients.
Concern has been raised by former NMH master Dr Peter Boylan that IVF treatment may not be permitted at the planned St Vincent's hospital site as it's owned by the Sisters of Charity.
The Catholic Church is against IVF treatment.
Dr Mahony has rejected Dr Boylan's concern, repeatedly insisting the new hospital will have "clinical independence".
Meanwhile, a senior source with knowledge of the project pointed to the provision of assisted conception facilities in the hospitals plans. They said this highlights the "absolute independence" of the hospital to provide services to women, despite arguments made to the contrary in recent days.
Architects' drawings for the new hospital show that fertility services are to be located on the first floor, which accommodates a 'reproductive medicine facility'.
This includes a 'cryo store' and 'embryology lab' and several procedure suites.
It is unclear what space at the hospital, if any, will be set aside specifically for Merrion Fertility Clinic.
The Department of Health appeared unaware the clinic would be moving there when first asked if it would be.
But a statement from Merrion Fertility Clinic confirmed it "will be moving to St Vincent's as part of the National Maternity Hospital Project". It said the "finer details" are under consideration and won't be finalised for some time.
Prof Wingfield said their "close affiliation" with the NMH will continue at the new site.
The Irish Independent asked if there is concern services the clinic currently offers won't be permitted at the St Vincent's site.
Prof Wingfield said the clinic "follows international guidelines for best practice in gynaecological and infertility care. This will not change when the NMH, including its fertility services, moves."
She added: "The enhanced facilities at the new hospital will, in fact, benefit our patients."
She said that the clinic will "continue to advocate for increased Government support for public funding for assisted reproduction services and for the urgent need for national legislation in this area."
The Department of Health said no provision has been made in the new hospital's design for the Merrion Fertility Clinic. Asked if the department was unaware that the clinic planned to move there, a spokesman later said there's an area for assisted conception. But he added: "It is not possible at this early stage to answer detailed questions regarding the operation of the new hospital."
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