SIPTU and the Irish Medical Organisation have strongly criticised proposals to deal with Emergency Department overcrowding which were agreed with the Irish Nurses and Midwives Organisation.
Both groups object to the HSE excluding all unions other than the INMO from meetings on the issue.
They have appealed to the Workplace Relations Commission, which brokered the proposals, for an urgent intervention in the dispute.
The WRC proposals include provision for frequent Emergency Department consultative forums at national, group and local hospital level to manage overcrowding.
On 26 January, HSE Head of Corporate Employee Relations John Delamere sent a memo to the Director of HR for hospital groups saying it was "appropriate" that other relevant stakeholders be involved, in line with normal collective arrangements.
He cited the example of SIPTU, which also represents nurses.
However, three days later, the invitation was rescinded in a memo stating: “The process set out in the WRC document of 11 January relates to engagement with INMO officials and members only."
INMO General Secretary Liam Doran has confirmed he urged the HSE to withdraw the invitation to other unions.
He said the WRC proposals were in response to a dispute between the INMO and the HSE - with no other parties involved in that dispute.
Mr Doran said the WRC agreement is clear as to who should attend.
HSE sources confirmed that they have written to WRC Director of Conciliation Anna Perry seeking an intervention in a bid to devise a mechanism to allow the concerns of all the parties to be addressed.
SIPTU Health Division Organiser Paul Bell has also written to the WRC seeking an urgent intervention regarding what it describes as SIPTU representatives being "dismissed" from the meetings.
In a further letter to HSE Director General Tony O'Brien today, Mr Bell describes the situation as unacceptable and intolerable, saying the union is now in dispute with the HSE.
He says SIPTU, which represents grades including nurses, radiographers, porters, cleaners and catering staff, will not cooperate with any decision which may emerge from management meetings.
He concludes by warning that the HSE must desist from discussing the terms and conditions of membership groups represented by SIPTU with any other organisation.
IMO Director of Industrial Relations Steve Tweed has also written to the Mr O’Brien, saying parts of the WRC proposals directly impinge on the clinical autonomy of members, especially consultants.
He says it is unusual for a proposal to be implemented that would directly impact IMO members, and members of other unions, when they were not party to the negotiations, and were not involved in any of the group wide or local hospital mechanisms set out in the proposal.
Mr Tweed also notes that the Emergency Department Forum has no jurisdiction to consider staffing or proactive rostering of clinical teams.
He notes the fact that the WRC proposals refer to the senior nurse manager having "autonomy to immediately address all issues to ensures patient flow" implies that the nurse manager has the right to overrule decisions on patient flow made by ED Consultants or Non-Consultant Hospital Doctors.
Mr Tweed describes this as unacceptable and intruding on the clinical autonomy of the ED consultant.
The IMO letter also states that staffing issues in non-emergency areas of the hospital should have equal if not higher priority.
Mr Tweed says it is essential the IMO has a representative on the ED Taskforce Implementation Group, the Group Wide Executive Forum, and each Hospital Local Forum.
The IMO also wants to be fully consulted on any proposed change that has the potential to affect members directly or indirectly.
A response from HSE management is awaited.
The result of the ballot by INMO members on the Workplace Relations Commission proposals is due on Friday.