The Council of Irish Medical Organisation has voted to recommend that its members reject the Lansdowne Road Agreement.
However, IMPACT and the Irish National Teachers' Organisation, two of the biggest public sector unions, have decided to recommend in favour of the agreement.
The IMO is to convene a ballot of members affected by the proposal on public sector pay restoration.
Dr Ray Walley, IMO President, said "this agreement does nothing to address the real crisis in our health services - the inability of the system to retain existing doctors and attract new doctors."
The Council has also expressed concern that the agreement does not treat all workers fairly.
Dr Walley said, while it is right that there should be an emphasis on the lower paid, it is important all workers in the health services receive acknowledgement for their efforts.
He added if we truly want to reform our services we need to keep doctors in Ireland.
The agreement, made last week after lengthy talks, will see public servants receive a €2,000 pay increase over two years.
The protections of the Haddington Road Agreement are also to be extended to September 2018.
The IMO had earlier expressed disappointment at the outcome of the talks.
Yesterday, the Teachers' Union of Ireland said it is to recommend rejection agreement when it ballots its members on the deal in the autumn.
The decision was taken at a meeting of the union's executive.
