The Ministry for Primary Industries (MPI) is seizing plant material from five apple and stone fruit nurseries across the country, as a precautionary measure against biosecurity risks.
The seizures some after an audit found incorrect record keeping at a US facility which is responsible for screening apple and stone fruit plant cuttings before they are imported.
MPI response manager John Brightwell said following the March audit, it put an immediate stop to imports and began tracing plants imported from Clean Plant Centre Northwest - Fruit Trees.
Mr Brightwell said about 55,000 plants had been traced and five affected nurseries and a small number of growers were told plant material will be seized from their properties.
He said it was not thought the plants are infected with pests or diseases, but it was taking a precautionary approach.
"Managing biosecurity risk is our top priority, but we will also be working with the affected nurseries, growers and with industry, to retain the highest value material if it is possible to do so.
"However, it is likely that many of the imported cultivars will need to be destroyed," he said.
Mr Brightwell said US authorities had treated the matter seriously and were conducting their own investigation.