A High Court judge has found the Ministry for Primary Industries made unlawful decisions in ordering apple and stonefruit growers to destroy tens of thousands of plants it deemed a biosecurity risk.

However, Francis Justice Cooke said the diligence and care demonstrated in MPI's decision papers could not be faulted.

He encouraged MPI and the industries to work together to develop and agree on a more appropriate set of directions to address MPI's biosecurity concerns.

The judgment followed a two-day hearing in which a group of growers sought an urgent judicial review at the High Court in Wellington of the MPI directive for nurseries and orchards to contain or destroy 48,000 apple and stonefruit plants derived from plant material imported from a quarantine centre at Washington State University.

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The directive under the Biosecurity Act included original plant material imported between 2012 and 2017 and extended to budwood and propagated materials derived from the original plants, the group said.

The directive affected 32 orchardists, nurseries, importers and intellectual property companies in Hawke's Bay, Waikato, Nelson and Central Otago.

Justice Cooke concluded decisions made by MPI under section 116 of the Act were unlawfully made.

But MPI's decision papers demonstrated the ministry had been very careful to thoroughly research the situation and then determined what action it should take.

"Put another way, the decisions demonstrated that the ministry has acted reasonably.

"It may well be that the new exercise can be done with a level of cooperation with the industry now that the position has been before the court and the statutory provisions that allow for compensation have been identified as relevant."

Justice Cooke put in place an interim order at the close of the hearing requiring the parties to contain selected plant materials in a quarantine facility and to allow all other plant material to remain in situ and be subject to a spraying and/or netting programme agreed with MPI.

The interim order also protected the parties from prosecution for failing to comply with MPI's directive for five days following the judgment, which was handed down yesterday.

A spokesperson for the grower group said MPI had been approached with a view to discussions. Many plants had already been destroyed, she said.

MPI in a statement said it remained concerned at the biosecurity risk associated with the plant material.

The judge had found MPI had carefully and thoroughly researched the situation and its decisions were reasonable.

"However, he disagreed with the sections of the Biosecurity Act that we used. We will be carefully considering the judgment and our next steps and how to address the biosecurity risk that New Zealand still faces," MPI said.

MPI said its directive followed a routine audit of the Clean Plant Centre Northwest at Washington State University. The audit found a number of critical non-compliances.

The grower group claimed the directive was based on a paperwork issue and MPI had not provided any evidence of an actual biosecurity risk presented by the relevant plant material.

The group claimed potential future losses of up to $1.5 billion from the destruction order, and said it would set back innovation in the sector by up to 15 years.