Budgetary concerns have also been discussed in private meetings between Government officials and the HSE.
The Irish Times has seen the minutes of the Government and HSE oversight group which took place in October.
Officials were told that the board overseeing the 1.7 million euro project was trying to find "realistic construction timelines" after a new programme was given by the builders, Bam.
The board believes Bams programme is "not in line" with its contract.
The minutes of the meeting also reveal that because of the "exceptional level of claims" for additional costs by contractors, the projects contingency fund is now not sufficient for a project of this scale and complexity.
The National Paediatric Hospital Development board said it would need 15 million euro to defend itself against the high level of going claims being made by contractors.