The HSE had already run up a deficit of €24.5 million by the end of January of this year, with hospitals in particular struggling to stay within their budgets this year, figures show.

The health executive's latest financial report shows expenditure of €999.5 million against a budget of €975 million, leading to a deficit of €24.5 million on January 31.

The figures have been published as it emerged that pay savings of nearly €200 million under Haddington Road may not be delivered in the health service this year, leading to a reported stand-off between Health Minister James Reilly and Public Expenditure Minister Brendan Howlin.

The HSE's January performance management report says €20.2 million of the shortfall is in the hospital sector, with €5.9 million and €10.1 million of the hospital service deficit relating to hospital income generation and agency staffing levels respectively.

The report says €7.8 million of the hospitals' overrrun on agency staff relates to the cost of hiring agency medical staff.

The HSE says there is a 'significant issue nationally' relating to the recruitment of junior doctors, which is driving agency expenditure in certain hospitals.

"In addition to this, hospital income generation will be closely monitored over the coming weeks to ascertain if there is an emerging underlying income generation issue in 2014."

Galway University Hospital had the largest deficit at €1.8 million on January 31.

The HSE report says the hospital system is facing a challenging year in 2014, with legacy deficit issues (deficits left over from previous years) to be addressed this year.

Hospitals are expected to meet the full value of cost containment plans unachieved in 2013 of €56.5 million, 'in addition to the full value of savings measures that are to be delivered in 2014'.

The report says these current year measures include efficiencies relating to Haddington Road and hospital reconfiguration in addition to targets relating to private health insurance income, and other measure including delivery under the employment control framework and nurse bank initiatives.

Engagement with hospitals relating to 2014 cost savings measures is taking place, the HSE said.

A 'deep dive review' of individual hospital cost containment plans currently being undertaken, according to the report.