THE Labour Court has backed a claim from junior doctors to be paid an extra 25pc for working after midnight.
The HSE had opposed the demands, saying that the health services are already facing "huge financial pressures" and that it is required to make "additional savings of €1bn in its budget for 2014".
It also estimated that the cost of providing cover for patients following the reduction in junior doctors' weekly hours may exceed any reduction in the doctors' pay bill.
However, the Labour Court ruling, published in recent days, backs Non-Consultant Hospital Doctors (NCHD) in their pay claim.
Steve Tweed, of the Irish Medical Organisation (IMO), which represents the NCHDs, last night welcomed the court's recommendation, describing the junior doctors' pay demand as "an open-and-shut case".
He said that the ruling was binding on both sides.
The HSE was last night unable to comment on the Labour Court ruling and could not provide figures for the additional cost that would be incurred as a result.
Last October, junior doctors staged a one-day strike in support of their claim for the introduction of a maximum 48-hour week as required by EU law, but ignored by the HSE.
The IMO claimed that doctors worked 70 to 100 hours a week with many working single shifts of up to 36 hours.
Under a settlement which averted further strike action, the HSE agreed that no doctor will be forced to work a single continuous shift of more than 24 hours.
It also pledged that it will be in compliance with the maximum 48-hour week by the end of this year.
In order to achieve the maximum 48-hour week, the HSE required some NCHDs to move to a night-duty-based system, but refused to pay them the increased night-shift rate paid to other HSE staff who work after midnight.
Currently, junior doctors are contracted to be rostered between 8am to 9pm, with any additional work over 39 hours paid as overtime.
However, in an effort to pave the way for the maximum 48-hour week, the IMO agreed to move to a night roster system but only if they were paid the same 25pc shift rate that applies to other HSE staff.
Pay costs for junior doctors in 2012 came to €225m, of which €85m, or over one-third, was in overtime, according to the latest HSE figures.
The average overtime payment in 2012 per doctor was €35,584.
But the HSE estimated that the "cost of providing medical cover for patients in the new working arrangements might exceed current costs".
It is understood that the additional cost could be incurred through the recruitment of hundreds of junior doctors to take up the slack, though this is currently under negotiation.
However, the HSE could not provide the financial estimates to the Labour Court to back up this estimate, so the court rejected its argument.