Junior doctors warn losing more admin support will hurt patients as they will have less time to care for them.
Health New Zealand is asking for voluntary redundancies from admin and advisory staff, as it continues to cut costs.
A union representing junior doctors, Speciality Trainees of New Zealand, said the current hiring freeze on support staff had already loaded more paperwork on its members.
Union spokesperson Emma Littlehales said "so-called back-office redundancies" would impact frontline medical staff and their patients.
"Our members have already seen the effect of a hiring freeze on their work and how it has taken away practising time from them and increased their non-clinical hours. There is a real risk that this gets worse with these further cuts."
The government had committed to setting up a National Resident Medical Officers Support Framework, along with support services - but the union feared the cuts could put that support in jeopardy, she said.
The national framework was supposed to fix problems for trainee specialists moving around the country, switching leave, payroll and other systems.
"We are immensely worried that the proposed cuts will put that promised support at risk.
"Around two thirds of doctors' hours worked in New Zealand hospitals are worked by RMOs, the more of those hours that are lost to admin work means fewer hours available for treating patients."
Health New Zealand has declined to comment further while the process was underway, out of respect for individuals considering taking voluntary redundancy.
However, in an email to staff on Wednesday, chief executive Margie Apa said to be "sustainable", the public health system needed to live within its budgets.
"That means we need to move towards being a more efficient organisation, focusing our resources on the delivery of frontline healthcare," Apa said.
"It is now clear the initiatives already in place will not, by themselves, resolve the financial issue or ensure we have the right people in the right place."
As staff costs accounted for the biggest chunk of expenditure, Te Whatu Ora needed to further review its size and structure as part of its "reset", Apa wrote.
"We are therefore providing the opportunity for eligible staff to consider voluntary redundancy, ahead of more formal change consultation processes likely over the coming months."