More than 400 jobs could go as the Ministry for Primary Industries and the Ministry of Health look to cut their budgets.
The Ministry for Primary Industries is proposing cutting around 231 staff as part of a cost-cutting initiative.
Like many government departments, MPI is trying to cut 7.5 percent of its budget - and told staff in an email on Thursday it wanted to reduce staff numbers by an estimated 9 percent, including vacancies but also disestablishing roles.
The ministry is looking to reduce a total of 384 roles of which 40 percent are vacant.
Director-general Ray Smith told staff that department heads would meet with staff across the business on Thursday to discuss the proposals to improve efficiency.
Smith said the organisation had grown by more than 1100 people in the last five years, in areas like biosecurity, policy, trade and regulatory systems - but greater efficiency was needed.
"With programmes now bedding down across the organisation and in the current fiscal environment, we need to make some efficiencies and change the way we operate while still delivering the excellent service and support our sectors require and expect."
He said it would not propose any reductions to frontline services and statutory roles, including veterinarians, animal welfare, fishery and food compliance officers, or our biosecurity teams at the border.
"However, we are proposing changes to roles and reporting lines in other areas of MPI, including the disestablishment of some positions."
Consultation runs from Thursday to 9 April, with final decisions expected by mid-May.
Meanwhile, almost 200 jobs could go from the Ministry of Health.
Staff were told about a proposal for organisational change at a meeting on Thursday as the ministry responded to the government's direction to cut 6.5 percent from its budget.
Just over a quarter of jobs or 180 roles could go.
Director of the ministry's Transformation Management Office, Geoff Short said some positions would be disestablished and some existing vacancies would not be filled.
There had already been a hiring freeze but that had not made enough savings.
Staff were told they would receive more details on the planned changes on 5 April, and a three week consultation period would follow.
It was a difficult and unsettling time for staff, Short said.
Minister for the Public Service Nicola Willis said on Thursday she could not yet say how many public servants would lose their jobs overall.
"I don't have that number yet. I expect that there will be people who will lose their jobs as we prioritise funding for frontline services."
She said her heart went out to people who could be made redundant, but said public agencies had known for some time their back office staffing levels were unsustainable.
"These are skilled, capable people and I am sure that there will be other job opportunities."
Prime Minister Christopher Luxon said it was a "very tough" day for people whose jobs were affected.
However, he said the government needed to "right size" the public service.
He said the Labour government had added 16,000 extra public servants and increased government spending by 84 percent during its time in power.
"This is the reality, we have to get government spending under control."
Agencies needed to "stop doing dumb stuff" and cull the programmes that were not working, Luxon said.
They had also been told to stop spending on consultants and make their back offices as efficient as possible.
The full scale of the government's public service cuts will be revealed in May's Budget.
'Terrible', 'horrific' - Labour
Labour's Health spokesperson Ayesha Verrall said it was "terrible news" for public servants from multiple departments today.
"As well as the country being in recession, the impacts on Wellington will be particularly tough when there are a number of people losing their jobs right here."
"Ministry of Health staff led the response to the pandemic. In addition they make sure that we have safely regulated medicines. They make sure that our health regulations of all sorts - including fluoridation - are functional. And they do things like taking steps to improve cancer care in New Zealand by working across our system."
She did not think the MOH could be as effective with the level of cuts proposed.
"Absolutely not. I find it impossible to believe that you could cut 25 percent of the positions in the Ministry of Health and that not have an impact on the safety of medicines in New Zealand, on the way in which our health system is regulated and on important aspects of cancer care."
Trade spokesperson Damien O'Connor, who was also the previous agriculture minister, said it was "pretty horrifying really".
"And it's no surprise - if you're going to have to fund tax cuts for landlords, the money's got to come from somewhere and this is from frontline services across MPI.
"It's not a bloated agency at all. Some of these people worked with Cyclone Gabrielle on the ground providing direct feedback to government and they were the frontline people that were helping those communities. If we're going to see cuts there, when we see climatic events occurring this will hurt all rural communities."
He was unsure which roles would be cut, but said MPI was the "heart of economic development and exports for our country and it just seems crazy".
"Clearly the M Bovis programme is shifting and it could be some people go from that area. But in terms of fisheries management, biosecurity, food safety, these are all critical areas of government responsibility.
"There are many people who are actually working on trade negotiations, ensuring that all the produce of the farmers and horticulturists produce can get through the trade barriers."
He said he did not believe MPI chief executive Ray Smith's suggestion the cuts would all come from back-office roles that would not affect frontline delivery.
"Look, I'm sure there are some vacancies that don't have to be refilled, I'm sure there are some reductions that can occur, but 10 percent, and then pretend that you're going to maintain frontline services? It's just not credible.
"I know that pressure is on all of those people - they need backup certification, they need verification, they need to be able to do their jobs properly."
'Good' - ACT Party
The ACT Party celebrated the news with a post on social media saying the news of the MPI cuts was "Good. The number of bureaucrats at MPI increased by 52% - or 1277 - between 2017-23. The average salary at MPI is about $102,000."
The post was re-shared by leader David Seymour.
Willis said she was "not responsible for David Seymour's comments".
"And as I said, my heart goes out to anyone who loses their job ... that's the reaction from ACT New Zealand, what he notes there is that the number of roles at MPI had increased significantly and as I said, it is good that our government is ensuring that resources go to the frontline."
O'Connor said it was to be expected from ACT.
"They think that less officials is better. When it comes to the area of exporting food and produce we need to be able to show and prove that it's been produced in he right way, that it's safe and that it's true to label ... we need MPI to do that work."
Verrall said: "These are real people who work for the service of our country, and when they are facing redundancies I think we need to express gratitude for the service that they have done".