The HSE is projecting a deficit of nearly €104m by the end of the year, based on the trends for the first five months of 2013, according to its latest monthly performance report.
The biggest overruns are expected in hospitals, amounting to €75m, and the Primary Care Reimbursement Scheme, which includes medical cards, where the overrun could be €25m.
Hospitals and community services have been asked to find extra cost containment measures.
The HSE is also in talks with the Department of Health on "potential contingency measures" aimed at reducing the projected deficits in the medical card and related schemes.
According to the HSE Chief Executive's latest report to the HSE Board, the service is reporting a deficit of nearly €50m to the end of May.
However, it says that the surpluses under a number of headings are in most cases expected to reverse by year end.
It says that within this is a core deficit of over €29m, when account is taken of timing issues around the phasing of budgets and the shortfall in retirees to the end of May, resulting in lower-than-targeted pay savings.
Another factor contributing to the overspend is the significant and extended pressures on Emergency Departments during the first four months of the year.
The delay in implementing cuts in fees to GPs and pharmacists has resulted in a shortfall of €10m.
The report warns that the current risk assessment would indicate a minimum projected deficit of €65m for the Primary Care Reimbursement Scheme, with the worst case scenario being an overspend of over €100m.
It also says that at this point, it is not possible to say if the full €150m in savings expected this year under the Haddington Road Agreement and built into the 2013 HSE Service Plan calculations will be delivered.
The full extra €60m in income expected from legislation to charge all private patients in public beds may also not materialise.
At the end of last year, the HSE received a €360m gross supplementary budget from the Government to deal with its overspending.
The hospitals with the biggest overspend up to the end of May are: University Hospital Limerick, at €3.1m over budget; St Vincent's University Hospital Dublin, €3m over budget; St James's Hospital Dublin, €3m over budget; Galway University Hospital, €1.7m over budget; Portiuncula Hospital, €1.4m over; and Tallaght Hospital, at €1m over budget.