The Ministry for Primary Industries (MPI) has ordered the seizure of 55,000 fruit plants across the country, after it was found the paperwork allowing them into the country in the first place was incorrect.
Industry members have slammed the move and say it's over the top.
"Some of the material may have to be destroyed - that would be unfortunate, but it may have to happen," said MPI director of plants and pathways Peter Thomson.
"The very worst case is if we did nothing and a disease was present in the material and it got out."
The "material" is any budwood or tree that has come from apple and stone fruit cuttings imported from a Washington facility between 2012 and 2017.
"The facility that was sending us material was supposed to be doing testing for some important diseases and they weren't doing it," Mr Thomson said.
"Our audit uncovered there were missing records, records that we just couldn't trust were true."
MPI has traced cuttings to six nurseries and 19 growers across New Zealand where the 55,000 affected plants will be seized, tested - and if necessary, destroyed.
It's an action plan the nursery industry says will come at a huge cost.
"There's two parts to that, one is the immediate value of the trees that'll be seized - but these are very important new varieties for the fruit industries," said Plant Producers Incorporated CEO Matt Dolan.
"Not having these varieties available for fruit production in the future could cost the industry."
The organisation that represents apple and pear growers says MPI's action is over the top, while Summerfruit New Zealand says its biggest concern is the unnecessary destruction of high value material.
"We'd like to see some really good processes in place in the next stages to make sure the material is properly tested and can be reintroduced," said Mr Dolan.
"Biosecurity is our number one concern, it has to be," said Mr Thomson.
"We're as concerned as they are about the loss of this important nursery material, but we've got to look after the disease risk first."
MPI says compensation has not been ruled out.