Remedial action was taken at Letterkenny General Hospital after a previous flooding incident at the new medical block prior to its opening in December 2011, it has been confirmed.
At a briefing on the situation at the hospital following last Friday's flooding, HSE Director of Communications Paul Connors said the work centred on a culvert near the new building,
However, he said an independent civil engineering review is currently being carried out, and until it is completed he would not speculate about what happened.
He said that something clearly did not work, but there had been unprecedented rainfall, which also has to be taken into account.
Meanwhile, the hospital's general manager, Sean Murphy, has said the hospital is working on implementing a temporary emergency department following flooding last Friday.
Speaking on RTÉ's News At One, Mr Murphy said it could take a number of months for the hospital's emergency services to be fully operational again.
However, Mr Murphy would not put a timescale on when the new facility would be in place.
The hospital is closed to all visitors and emergency admissions have been diverted to Sligo and Derry.
Mr Murphy said: "At the moment, we have lost a very significant proportion of our hospital. About 40% of our hospital has been flooded with contaminated water. This isn't just a mopping up operation."
Mr Murphy said 1,600 outpatients are normally seen in a week in Letterkenny.
He said contingency arrangements have been made for about two thirds of them, either on site or in other locations.
Around 350 day cases are also normally seen in a week at the hospital, including 120 cancer patients who are on chemotherapy regimes.
This has been maintained and their care has not been compromised, Mr Murphy said.
About 200 dialysis treatments are also given every week and these are also continuing.
Mr Murphy said the biggest challenge is radiological and diagnostic support, with virtually no radiological capacity available.
A number of mobile units are being transported to the hospital, and Mr Murphy hopes to have them on site by the end of the week, with a mobile MRI on site by next week.
Mr Murphy would not confirm suggestions that part of the old building, where the temporary emergency department is to be established, will have to be knocked because of contaminated asbestos.
The Health Service Executive earlier said it expects the current arrangements to continue for several weeks.
However, Irish Association for Emergency Medicine spokesman Fergal Hickey said he believes it could take much longer.
He said experience elsewhere of hospitals damaged by flooding would suggest facilities at Letterkenny will remain closed for months rather than weeks.
Speaking on RTÉ's Morning Ireland, the Sligo Regional Hospital consultant said for some of the reconstruction work a time frame of weeks was optimistic.
He said much of the supporting infrastructure around the emergency department at Letterkenny had been damaged by the recent flooding.
The damage included the radiology department and the kitchen being put out of action.
Dr Hickey said the HSE should issue daily updates to people in the hospital's catchment area.