A group representing apple and stonefruit growers and other fruit industry participants challenged the directive last month, seeking a High Court judicial review.
The group claimed the directive would cost the industry up to $500m in lost income and would set its innovation progress back by 15 years. Meanwhile, it said, plants and plant material were dying because they could not be planted or used and many plants had been destroyed.
The High Court found the legal route taken by MPI to make the containment/destruction order was unlawful, but noted the thoroughness of MPI's investigations. The court recommended the parties negotiate a solution - a finding which MPI sought a time extension for, which has now expired.
The MPI statement said the ministry remained concerned at the potential biosecurity risk associated with the imported plant material.
"We've now issued new notices under a different section of the Biosecurity Act so we can continue to manage potential risk through containment and a spraying and netting programme while we work through a testing plan with each owner," the statement said.
"If no pests or diseases of concern are found then the plant material will be able to be released in the future.
"MPI remains open to receiving modest reimbursement claims for some direct and verifiable losses incurred as a result of destroyed or contained plant material."
The sector group challenging MPI's directive has been approached for comment.