Mr Wagstaff said the cut would weaken and remove crucial management of agricultural, biosecurity, fisheries and forestry systems which protected New Zealand.
"Some of those skilled people will go overseas, so the loss of knowledge and expertise won't just be to the public service, it will be to the whole of New Zealand industry,'' he said.
The Government was in danger of repeating the 1990s restructurings, "when the loss of knowledge, expertise and adequate staffing levels in the public service led to disasters, and economic costs for the whole country''.
In 1995, the Ministry of Fisheries was split off from the Ministry of Agriculture and Fisheries, and in 1997, forestry was folded into agriculture to create the Ministry of Agriculture and Forestry. Since then, a standalone Food Safety Authority was split off from MAF and the Ministry of Health, only to be blended back into MAF last year.
Mr Wagstaff said MAF was slashing hundreds of jobs in a bid to save $18 million to cope with the Government's indiscriminate and unjustified public service budget cuts.
Labour's acting state services spokesman, Grant Robertson, said the job cuts came on the back of thousands of jobs being axed across the public sector in organisations as diverse as Defence, Inland Revenue, and KiwiRail.
"They are a direct result of this Government's carve-up of the public sector, and simply add to the increasing number of unemployed Kiwis,'' Mr Robertson said. In the past year alone more than 1500 state sector jobs have been axed.
"The Government needs to tread carefully in an area as important as our agricultural sector so that they do not reduce vital services in their search for funding cuts,'' Mr Robertson said.
State Services Minister Tony Ryall said in March that MAF and the fisheries ministry would be merged by February 1.
Rural lobby group Federated Farmers had previously called for a "super'' primary industries ministry.
MAF director-general Wayne McNee said there was no plan to cut numbers of fishery officers, animal welfare inspectors and investigators, and quarantine inspectors.
"We will continue to deliver the front-line services that we know are valued by New Zealanders, and ensure these are of a high standard,'' he said.
- NZPA