Support staff in the health service and emergency department workers are to be balloted on strike action by Siptu.
Siptu says it is because the HSE has failed to implement parts of the Lansdowne Road agreement on public sector pay for the 25,000 support staff.
The union said it will be followed by a ballot of emergency department workers in selected hospitals on Monday, January 23.
That ballot is because the HSE has not given concessions to other grades in emergency departments outside of nurses.
Siptu's Paul Bell, said: "It is deeply regrettable that our members feel compelled to take this action. The dispute involving support staff has been brought about by the HSE and Department refusing to implement fully binding provisions of the Lansdowne Road Agreement and Haddington Road Agreement.
"Our members overwhelmingly supported these agreements in good faith."
He said they have been "pushed to the brink" by the HSE's refusal to reintroduce a job evaluation scheme, to pay interns, apply incremental credit and double time payments.
He said: "The failure to implement these sections of the agreements have been particularly evident in the HSE South area which includes County Cork and County Kerry.
"Since late 2015, Siptu Health representatives have been informing the HSE of our members' concerns in regard to these issues. However, they have encountered obstruction and confrontation in response to their attempts to secure the implementation of these key elements of the respective agreements."
He also spoke about the ballot in relation to the concessions made by the HSE to nurses working in emergency departments that have not been extended to other workers.
He said: "This ballot for strike action will involve all grades working in emergency departments and be conducted in selected hospitals throughout the country with a particular focus on facilities in Dublin, Cork, Galway and the Midlands.
"Siptu will publish the hospitals which will be affected by this ballot in the coming days."