The Ministry for Primary Industries (MPI) says it is undergoing what it calls a realignment of its current structure.
The Labour Party says it is a major restructuring proposal that has left staff shellshocked the week before Christmas.
MPI director-general Martyn Dunne issued a statement on Friday but has refused to be interviewed about the proposal.
He said he announced to staff this week the intention to investigate any improvements that could be made, which may lead to what he called "shifts in alignment".
Mr Dunne said it was not an opportunity to downsize, but follows recommendations resulting from a food safety scare earlier this year.
Labour said the announcement caused unnecessary stress for staff as they prepared for the Christmas break, including the prospect for some of having to take up a position overseas at short notice.
Primary Industries spokesperson Damien O'Connor said the report identified problems with food safety and biosecurity - and that was where he believed changes could be made.
"The minister should front up and say [if he is] ... going to pull out food safety, [if he is] ... going to pull out biosecurity and have two robust Crown entities taking care of very important issues for New Zealand into the future," Mr O'Connor said.
"That would be the kind of restructure we would consider beneficial, but I guess he's going to try and shift the chairs around again."
Mr O'Connor said 200 jobs had been lost in MPI restructuring in the past two years.
