Irish Rail train drivers with the National Bus and Railworkers union and Siptu are going ahead with a ballot for industrial action.
The decision was taken at a meeting of train drivers this afternoon in Dublin.
The unions said they were ballotting drivers because the company has failed to fulfill a commitment to reward past productivity increases.
The ballot result is due on October 5.
Irish Rail has described the move as "disappointing".
The company says it suggested asking the Labour Court to decide on the pay issue, but the union rejected this.