The Health Service Executive is reporting a current gross deficit of €93.7 million and estimating a year-end deficit of around €105 million.
This deficit figure could rise further, due to lower than expected savings in health under the Haddington Road Agreement and advance payments from private health insurers not now expected until 2014.
According to a monthly performance report there are 45,155 adults and children waiting for day case or inpatient procedures.
A further 7,000 to 8,000 patients are waiting for a gastro-intestinal endoscopy.
The report shows that there are also 374,104 patients waiting to be seen for the first time by a consultant at an outpatient department.
Of these, 2,236 patients are waiting four years or more and over 84,000 are waiting for a year or more to be seen.
Under a recent policy, patients who do not attend an appointment will be contacted along with their GP and if there is no reply, the patient will be taken off the outpatient waiting list.
The HSE says that waiting lists are falling.
The report shows that 86% of all adults are waiting less than eight months and 79% of all children less than 20 weeks for a day case or inpatient procedure.
The hospitals most heavily overspent are: St James's in Dublin, at €10m over budget; St Vincent's, €8.6m over; Galway University Hospital, €7.2m; Limerick Regional, €6.4m; and Cork University Hospital, at €6m over.
The HSE says the overspend at St Vincent's is due to an extra 60 beds being opened to cope with the complexity of cases presenting at the Emergency Department.
The HSE Director General has written to all hospitals over budget asking them to bring their spending back into line before the end of the year.
There are now 75,020 people with a discretionary medical card or GP visit card - nearly 4,000 fewer than last year.
The HSE says some of these people will now have been given a full medical card or GP visit card.