The future of 89 Ministry of Health staff members is uncertain following the restructuring of the unit that offers health policy advice to the Government.
The ministry says staff numbers will remain largely unchanged, but the Public Service Association believes redundancies could be substantial.
The Health Ministry has been studying how to improve its policy advice role, in the wake of the creation of several business units within the organisation and the re-emphasis of its core role of policy advice for the Government.
It has also been told its current policy advice is poor and must be improved.
Acting ministry head Andrew Bridgman says from February next year, policy advice will be consolidated into one unit with a separate unit focusing on clinical advice, led by a new chief medical officer.
The new structure has 90 jobs, and the current 89 staff are to be matched to them or redeployed if possible.
The ministry says redundancy will not be considered until all other options have been considered.
But the PSA says the review on which the decisions have been based is flawed.
Senior policy staff are being targeted and it will result in a loss of expertise from a key ministry, it says.
The union says 150 of its members are affected.