The director-general of the new Ministry of Agriculture and Forestry says a merger resulting in 144 job losses will make the agency more effective.
MAF estimates cutting 241 positions, 97 of which are currently vacant, will save it more than $18 million over the 2012-13 financial year.
The cuts are the result of a merger of the Food Safety Authority, and the ministries of agriculture and forestry, and fisheries.
Staff at the Auckland and Wellington MAF offices were told on Wednesday morning about the restructuring.
MAF director-general Wayne McNee says most of the positions going will be at head office level and stem from combining functions such as financial management, policy advice and communications.
Mr McNee says there are no proposals to reduce the number of front-line staff working as fishery officers, animal welfare inspectors and quarantine inspectors.
"We're looking at making the ministry much better connected than it's been in the past. It has been an effective and efficient ministry, but quite siloed in the way that it works.
"We're really looking at making the different parts of the organisation - like the science, the policy, the standards - work closely with out front-line, so that everybody's working together."
However, the Public Service Association says the loss of the positions at MAF will mean delays in scientific back-up to front-line biosecurity staff at New Zealand's borders.
The union's national secretary, Richard Wagstaff, says even though no front-line border control jobs will go, the staff reduction is likely to mean there will now be delays to the prompt scientific back-up that border control officers need.
"Those people at the front-line looking at things coming into the country - new diseases and new bugs and so on - they need prompt and immediate scientific back-up and support.
"If those jobs are going to be cut, then they're not going to be able to get the support they currently have."
A new organisational structure is expected to be complete by October this year.