Iarnród Éireann staff belonging to the National Bus and Rail Union have overwhelmingly rejected cost reduction measures, including pay cuts proposed by the Labour Court.
The proposals, which included pay cuts over the next two years and four months of up to 6.1%, were rejected by 75% on a turnout of 90%.
SIPTU, which represents 1,900 of the company's 3,767 employees, narrowly rejected the proposals last week by a margin of 51% to 49%.
SIPTU is currently balloting its members for industrial action or strike action in the event that the company moves unilaterally to introduce the cuts.
The Transport and Salaried Staff Association, which represents 324 clerical and administrative staff, voted to accept the proposals by a margin of 72%.
The 400 members of the Technical Engineering and Electrical Union also accepted the proposals, as did most of the members of Unite.
The compromise Labour Court proposals shortened the duration of pay cuts from three years to two years and four months, reducing the scale of savings that would be delivered to the company.
However, the Labour Court warned that the cuts were essential for the viability of the company.
It will now be a matter for the company to decide whether to unilaterally implement changes.
Earlier, Minister for Transport Leo Varadkar said delays in implementing cost savings at the company will not be allowed to continue indefinitely.
He said cost savings needed to be made to protect jobs at the company and to protect rail services for the public.