The European Commission has decided to refer Ireland to the EU's Court of Justice for not complying with rules on limits to working time.
The complaint is mainly focused on the hours worked by junior doctors in public health services.
The Commission said that Ireland is failing to ensure that in practice junior doctors work no more than 48 hours per week on average, including any overtime.
It said that junior doctors are regularly required to work an average of 70-75 hours per week, without adequate breaks for rest or sleep.
Minister for Health James Reilly this afternoon said the Government was committed to achieving compliance with the European Working Time Directive for junior doctors by the end of 2014.
In a statement, he said he was disappointed at the decision to refer Ireland to the ECJ.
He said: "I have met with the Commissioner for Employment, Social Affairs and Inclusion, Mr Andor, on two occasions and have used those meetings to emphasise Ireland's commitment to achieving compliance with this Directive. This remains the position of the Irish Government."
The minister added: "At my request, the Health Service Executive has made attainment of EWTD compliance a top priority in 2013 and this will continue until full compliance is achieved.
"Already, good progress has been made in relation to reducing the number of doctors working more than 68 hours per week and the incidence of shifts longer than 24 hours."
The Irish Medical Organisation has welcomed the Commission's decision.
IMO Director of Industrial Relations Steve Tweed said: "While it's shameful that failure of the HSE and Department of Health on this issue has led to this, we welcome the decision of the EU as we believe it will fundamentally alter the attitude of the HSE on the matter.
"The HSE has always tried to sweep this issue under the carpet but will now be forced to answer on it by the court."