The HSE says it has identified ten hospitals where significant risk issues have arisen in relation to matters raised in reports from the Health Information and Quality Authority.
The executive revealed the details in a submission to the Oireachtas Committee of Public Accounts today.
The ten hospitals are: Our Lady's in Navan, Louth County, Midland Regional in Portlaoise, St Columcille's in Loughlinstown, Mallow General, Bantry General, Ennis General, Nenagh General, St John's in Limerick and Roscommon County.
The HSE said that some of the hospitals had already completed the process of addressing the clinical risks identified.
The four hospitals where risks are still being addressed are Portlaoise, St Columcille's, Bantry and St John's in Limerick.
In response, the chief executive of St John's said that the hospital board took a decision last March to transfer all ICU care to the acute Mid-Western Regional Hospital in Limerick. He said that process is ongoing and they are working with the HSE to achieve this.
The HSE has said that there are issues in relation to the remoteness of Bantry Hospital.
There is no emergency medicine consultant or Intensive Care Unit there and it is not possible to ventilate patients overnight.
As a result, the future model and range of surgery is being examined.
In relation to St Columcille's, the executive has said that critical care patients will go to St Vincent's University Hospital from November when 24-hour emergency department cover ends.
The volume and complexity of surgery is under review at Portlaoise, while at St John's in Limerick arrangements are advanced to transfer critical care to Limerick Regional.
HSE Chief Executive Cathal Magee told the PAC said that smaller hospitals will not be closed and their importance will not be reduced.
He said that HSE was not overseeing the demise of smaller hospitals and that it was 'change for safety, not change for downgrading'.
The committee was told that there are now 158 vacant junior doctor posts around the country.
Mr Magee said that the numbers presenting to emergency departments are on the increase and said it was unacceptable that patients were forced to wait on trolleys.
Last year, 1.1m people presented themselves at the country's 33 emergency departments, one third of which were subsequently admitted to the main hospitals.
Mr Magee said this year there has been an increase of 5,000 when compared to the same period during 2010.
He said that the shortages are likely to especially affect smaller hospitals, but that the HSE has contingency measures in place to ensure patient safety.
Mr Magee said the full picture would be clearer next Monday, which is the traditional date when junior doctors change posts.
He also said the HSE was looking to recruit a further 14 consultants in emergency medicine.
Elsewhere, Sinn Féin President Gerry Adams, TD, has said that 'the health service is in crisis and the Government's response is to cut budgets, cut services and hand hundreds of millions of tax payers money over to unguaranteed bond holders in toxic banks.'
322 patients on trolleys this morning - INMO
322 patients were waiting on trolleys in the country's 33 hospital emergency departments this morning, according to Irish Nurses and Midwives Organisation figures.
The hospital with the largest number waiting was Beaumont Hospital in Dublin which had 34 patients on trolleys, followed by Cavan General with 29.
Both Cork University Hospital and Our Lady of Lourdes in Drogheda had 27 patients waiting this morning.