The HSE said hospitals had racked up €63m of the €80m deficit at the end of March.
The overall deficit is significantly higher than the €26.7m reported over the same period last year.
Almost 40% of the overspend by hospitals was caused by income shortfalls (€10m) and increased costs of agency staff (€14m).
The hospitals with the biggest budget overspend are:
* University Hospital Limerick €5.9m.
* Waterford Regional Hospital €4m.
* Mater Hospital, Dublin €3.8m.
* Galway University Hospital €3.3m
* St Vincent’s University Hospital, Dublin. €2.8m.
The health authority said the National Service Plan clearly showed it was facing the most “severe” financial challenge this year.
The report shows spending over the first three months of 2014 at €2.97bn which is lower than the €3.08bn reported over the same period last year.
However, it only had a budget of €2.88bn for the period which was less than what was spent.
The report points out that the HSE’s budget has been cut by 27% — €4bn over the past seven years.
It said the number of new attendances at emergency units had increased by 8,225 over the first three months, a 3% increases and the number admitted as in-patients from emergency departments had risen by 1,583 — a 2% increase.
Admissions through medical assessment units had risen by 1,250 – 16% higher than last year.
However, the number of people on emergency department trolleys while waiting on a ward bed had decreased by 3% compared with the same period last year.
The number of people admitted for planned procedures is 3% (753 people) lower for the first three months of the year compared with the same period last year.
A total of 24,285 people have been admitted for scheduled hospital care up to the end of March. However, the number of people in hospital on a day care basis is 1% (3,077 people) lower than the same period last year. A total of 202,815 people had been treated in hospital on a day care basis up to the end of March.
At the end of March, 46,000 people were waiting for an in-patient or day care hospital procedure, with one in 10 waiting over eight months.
According to the report, 4,532 children are waiting for an in-patient or day care procedure and almost one in five are waiting more than five months.
There were 16,295 people waiting over a year for an out-patient appointment at the end of March — about 5% of all those waiting. Last year, 17% were waiting more than a year for an appointment.