Galway Bay fm newsroom - University Hospital Galway had to cancel 948 appointments over the course of this year - followed by Mercy University Hospital in Cork with 485.
The HSE says "capacity issues" are why 7 thousand procedures couldn't go ahead between January and September this year.
The figures released to the Irish Daily Mail show 25 operations were cancelled every day.
The Irish Medical Organisation says 5 thousand hospital beds will be needed over the next 20 years to deal with overcrowding problems.
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President of the IMO, Dr Peadar Gilligan, says a lot more investment is needed in the health service.
