Hospitals have been told to cut down on the numbers of patients they treat because they have overspent by more than €76.5m so far this year.
The HSE said hospitals have been treating more patients than they have been funded for and the numbers are up 4.7pc compared to this time last year.
Hospitals with some of the biggest deficits are Beaumont Hospital and the Mater Hospital in Dublin while Our Lady of Lourdes Hospital in Drogheda is also in the red.
The warning comes as the latest figures show 3,981 public patients are on waiting lists for surgery of over nine months.
There are more than 200,000 people on outpatient lists.