Nineteen hospitals around the State have had their collective budgets reduced by about €12 million for inefficiencies in their operations.
Tallaght hospital is the worst affected and will lose more than €2.8 million from its budget for the year. The adjustments to the hospital budgets are carried out annually under a system known as "casemix", which rewards efficient hospitals and penalises inefficient ones.
The Mater hospital in Dublin is to have its budget reduced by €2.1 million, while €1.17 million will be shaved from the allocation to St Columcille's in Loughlinstown.
St Luke's Hospital in Kilkenny, which is praised regularly by the Government for its efficient handling of patients in its A&E unit, will see its budget reduced by €899,000. At the same time, 17 hospitals will receive nearly €12 million in additional funding as a reward for efficiency.
St James's Hospital will receive an additional €1.818 million, while the allocations to Waterford Regional Hospital and the Longford-Westmeath General Hospital in Mullingar will rise by €1.1 million respectively.
The HSE said that "casemix" had been introduced to improve the quality and efficiency of the services provided to patients.
"It does so by measuring the performance of an individual hospital in terms of the numbers of patients treated and the costs of that treatment and comparing it with the performance of other hospitals across the country.
"It then rewards best performance by reallocating funding from hospitals that fail to meet the target for the number of patients treated to those hospitals that surpass their target levels," it stated.
The HSE said that hospitals were not penalised for long-stay patients and were not rewarded for discharging patients too early. It said the "casemix" system was designed "to take account of each hospital's 'unique issues and unique patients'. Casemix ensures that hospitals are funded for the patients they actually treat, at a cost per case determined by their own peers.
"Traditional acute hospital funding allocates funding in advance, although the exact mix of patients to be treated in any given year may not yet be known - including individual patients which may have cost millions of euro to treat," the HSE stated.
Among the other hospitals to lose out are Our Lady's hospital in Navan and Mayo hospital, which will have their allocations reduced by nearly €800,000.
The budgets for Cavan and Sligo General hospitals will be reduced by over €500,000. University College Hospital Galway and Letterkenny General Hospital will see their budgets increased by more than €900,000.