Mice were found on Zespri's first shipment to Europe for the season last month.
Since then the company has been sorting through the fruit to try and salvage as much as possible.
Chief operating officer Jason Te Brake said Zespri's inspected 2600 (54 percent) of the pallets.
It even sent staff to Belgium to help with the situation and engaged external food safety experts.
"It's become clear that we can't fully mitigate the potential food safety and reputational risk to the brand with enough certainty to release any fruit.
"Reworking this fruit would be a substantial and complex operational undertaking requiring considerable resources and time. Even then, we could not be sufficiently confident we could remove the risk associated with the presence of rodents. Our customers have also been clear they don't want the fruit because of the potential risks associated with it."
Based on this combination of factors, Zespri has decided to dispose of the fruit. It would be turned into biofuel, Te Brake said.
The total value of the fruit plus costs associated with reprocessing and disposal was estimated to be around $34 million
Te Brake said Zespri continued to engage with it's insurance and shipping partners.
"The value of recovery will not be known until the claims process is complete - a process which will take some time."
