More than 140 jobs are set to go at Ministry of Agriculture and Forestry as a result of a merger between MAF and Fisheries earlier this year.
Staff were told about the cuts this morning, with a final plan to be adopted in October.
Public Service Association national secretary Richard Wagstaff said cutting further jobs from the Ministry of Agriculture and Forestry would threaten some of New Zealand's most important industries.
He said 241 jobs were going, but there were 97 vacancies so redundancies were likely to number about 140.
The majority of the job cuts will be in Wellington where MAF has its head office, while Auckland is set to lose about 10 roles.
MAF said today it may also consolidate some offices in regions with more than one branch site as leases expired.
Wagstaff said the industries were critical to the New Zealand economy and "we shouldn't be putting them at risk."
"We're in danger of repeating the experience of the 1990s when the loss of knowledge, expertise and adequate staffing levels in the public service led to disasters, and economic costs for the whole country,"
MAF director-general Wayne McNee said he expected the changes, which include plans to combine financial management, policy advice and communications, to realise savings of more than $18 million in the 2012 - 2013 financial year - higher than earlier estimates.
The proposal does not affect fishery officers, animal welfare officers and investigators, or quarantine inspectors and would be made without reducing front line services, he said.
MAF and the Ministry of Fisheries merged on July 1 and an interim structure has been in place since.
Wagstaff said staff were anxious about their jobs and were worried how the business will continue to function.
"We understand something like 700 jobs have been identified as affected from well over 2000 jobs, which means some staff may have to change their reporting lines."
State Services Minister Tony Ryall said earlier this year creating a single entity would reduce administrative duplication and costs.
- Susie Nordqvist