The Mater Hospital has said that over €70 million in public money will have to be written off if the new National Children's Hospital is not located at the campus there.
Professor Brendan Kinsley, chairperson of the hospital's medical board, said that this money was spent preparing for the arrival of the new hospital.
He said that if it is written off it will have to be re-spent elsewhere on a new location.
Prof Kinsley said over €30m was spent by the National Paediatric Hospital Development Board, while €23m was spent on access and other services at the new adult hospital development.
A further €16m was spent in relation to the planned movement of Temple Street Children's Hospital to the Eccles Street site.
He said the Mater was happy that in its submission to the Dolphin Review it "ticked all the boxes" on site capacity.
He said the Mater site was chosen twice in reviews by international paediatric experts, including more recently in a review commissioned by the Minister for Health James Reilly in early 2011.
Prof Kinsley said the Dolphin Review, which consisted of solely Irish expertise, appeared to have come to a different conclusion and that local expertise was trumping international expertise.
He said the Mater wanted to ask the Government why potentially €70m is being written off and that the gold standard of tri-location, which the Mater can deliver on time by 2016, is being ignored.
Dolphin Review concerned over size of Mater site
The Dolphin Review expressed concern as to whether the Mater Hospital site was sufficiently large to accommodate a high-quality maternity hospital as well as the new National Children's Hospital.
Further details have emerged as to why the Mater site was not a frontrunner in the review, despite almost €50m being spent on the project there.
This was despite the site being significantly reworked, especially in terms of its height, since the rejection of planning permission by An Bord Pleanála.
After the Dolphin Review got under way, the Mater was able to include the offer of the 1861 building, a protected structure, for purposes such as research and education.
The Dolphin Review found that this would add space but not significantly on site capacity.
"Whether the site is sufficiently large to accommodate a high quality maternity hospital as well as a children's hospital remains a concern", the group concluded.
The review only considered those site proposals that were supported by a Dublin academic teaching hospital given that 70% of patients who will attend the new hospital will come from the greater Dublin area.
It found there was no single perfect solution and all three front runners had restricted sites to varying degrees, which were addressed in their proposals.
The Tallaght Hospital site proposal also had problems and the review found the site would be significantly constrained by the proximity of an existing apartment complex.
A Beaumont Hospital proposal also ran into trouble because it was located in a low-rise housing area and gaining planning permission approval for a large building up to ten storeys high could be problematic.
Also, construction of the children's hospital there could not start until the existing multi-storey public car park at Beaumont and other buildings were rebuilt elsewhere on the campus.
As revealed by RTÉ News this week, the Dolphin Review said that from a clinical and academic perspective, St James's Hospital is identified as the "existing Dublin area teaching hospital that best meets the criteria to be the adult partner in co-location because it has the broadest range of national specialties and excellent research and education infrastructure".
The report also said a corridor could link the new children's hospital on St James's to the existing Coombe Maternity Hospital, or a new maternity hospital at St James's.
A letter published today and signed by around 40 consultants at Our Lady's Children's Hospital in Crumlin says the new children's hospital should be physically linked to a maternity hospital as high-risk babies would require emergency medical care at the new hospital following their birth.
St James's has the smallest site for construction but has a greater site capacity overall.
The report found it has some drawbacks in terms of site suitability and is not without planning risk.
From a design and planning perspective, the sites adjoining Connolly and the Coombe offer the best potential for future expansion and a landscape setting, but the report finds that the proposed integration of Connolly with Beaumont and the RCSI and the universities would have to be accelerated.
It found access by car to Connolly to be excellent and bus services could be upgraded to meet demands.
The Dolphin Review received 41 site offers, the majority of which were greenfield.
It has advised the Government that a greenfield site would require very substantial investment with ramifications in terms of zoning, planning, procurement and time.