The High Court has validated MAF Biosecurity New Zealand's actions in allowing imports of honey products from Australia.
The Beekeepers Association of New Zealand had argued the organism Paenibacillus alvei (P alvei) could be found in honey imported from Western Australia.
It told the court the honey should be subject to strict Environmental Risk Management Authority (Erma) regulations before it was cleared.
MAF argued that as P alvei was a "passenger" organism it only needed to be checked by the less rigorous Biosecurity Act, regulated by MAF.
In his decision, released on Wednesday, Justice Simon France, recognised the challenges of preventing exotic pests and diseases entering New Zealand.
"It is common ground that new organisms will be brought into New Zealand, unknowingly and unknown, every day," he said.
"They will come as passenger organisms on people, their clothes and their goods.
"To be too absolute is to require the border to be shut to all traffic."
The National Beekeepers Association (NBA) said it was very disappointed with the decision and would take the case to the Court of Appeal.
"The NBA considers that it had a strong case to support its application," president Jane Lorimer said.
"The NBA has reflected on the judgment and decided to pursue the application through the Court of Appeal."
The High Court had also ordered the lifting of the current injunction on imported honey.
But since the decision was subject to appeal the injunction could stay in place for another five or six months.
Biosecurity Minister Jim Anderton welcomed the decision, which he said endorsed MAF's risk analysis and import health standard process.
He said the case was the latest attempt to prevent Australian honey entering New Zealand.
Mr Anderton said the court had obviously considered the pressures facing the wider biosecurity system operating in today's global trading environment.
"We can't stop trade and travel which is why we must focus on the management of risk to best protect our economy and environment," he said.