The Ministry of Health is proposing to cut 134 jobs to meet the government's demands to reduce costs, RNZ understands.
Meanwhile, the Ministry of Social Development (MSD) is calling for voluntary redundancies.
NZ Doctor earlier reported the Ministry of Health needed to reduce spending, and was expected to slash its budget by $78 million between 2023/24 and 2024/25.
More than a quarter of all positions could be directly affected.
Ministry of Health staff are meeting on Thursday and Friday to discuss the proposal. Consultation will close on 26 April and a final decision will be made in June.
Have you lost your job from the cost-cutting measures? Contact: jemima.huston@rnz.co.nz
At MSD, workers affected were in the service delivery and Māori communities and partnerships teams, as well as those in human resources, policy, strategy and communications.
The Public Service Association (PSA) said the voluntary redundancies, along with vacant roles not being filled, could see hundreds of workers leave.
Spokesperson Duane Leo said the government was out of touch and it was "disgraceful" to cut a workforce that supported so many New Zealanders.
Roles impacted include directorates in clinical community, mental health, evidence, research and innovation, Māori health, public health - some of which helped regulate the quality and safety of providers and products.
"They're important in terms of MedSafe, where they regulate medicines and medical devices, emergency management teams responsible for preparedness, leadership and assurance in health emergencies - these are all important directorates that are now suffering because of this proposal," Leo said.
MSD was the second largest public service employer, with around 9000 full-time equivalent employees.
"Every day we are seeing the fiction of 'no cuts to the frontline'," Leo said. "Make no mistake, those supporting New Zealanders and communities will be under more pressure than ever before. How can that be good for the care and support they provide?
"But the government would rather tie their hands behind their backs and fund tax cuts for landlords. Landlords don't need a handout - but the thousands of New Zealanders supported by case managers need to be helped out. And that means properly resourcing this critical agency across all areas."
Next week the Department of Conservation and the Department of Internal Affairs will announce their plans for cuts, and the following week Oranga Tamariki will do the same.
The PSA represented about 400 Ministry of Health staff, and national secretary Kerry Davies said such a big cull was heartless and cruel and could destabilise the health system.
"A lot of these people have been working for the ministry and formed very strong bonds - particularly during the Covid period, giving their all to meet the demands of that pandemic crisis for New Zealand," she said.
"The work that is needed to prepare for the health needs of the country - that's really serious, important work. It's the backbone of the health system."