The pests were discovered in the fruit holds of a charter vessel during standard clearance processes in Zeebrugge, Belgium.
There were about 1.2 million trays of SunGold onboard. Zespri's season forecast was for growers to be paid between $10 and $11.50 a tray, meaning the total shipment was worth about $12 million.
The fruit would be quarantined while inspections were under way, Zespri chief operating officer Jason Te Brake said.
"Unfortunately, there has been mice activity present within the vessel and it is to a reasonable extent.
"Now that we're finding quite a lot of contained product's been contaminated, so what we are doing now is assessing how much of the 4800 pellets of fruit have been impacted."
He said it was too early to say how much of the fruit will need to be dumped. The shipment accounts for 0.5 percent of the season's crop. It was a big blow for the marketing company, which was excited about exporting a bumper crop this season.
"Zespri takes fruit quality incredibly seriously - no fruit will be released unless both Zespri and relevant regulators are confident of mitigation measures."
Te Brake said the start of the season in Europe would be pushed back a week, with a second charter vessel due to arrive in Zeebrugge on Saturday.
"That fruit will undergo an inspection process before being released to customers. We're now working with our customers and our distribution partners to ensure we can commence the European sales season as quickly as possible to meet strong consumer demand."
Te Brake said this was the first time in two decades that Zespri had encountered the issue.
"We have a proven track record over 20 years of providing only the highest-quality fruit and building a brand people trust and we won't compromise on that.
"We have had a number of successful arrivals in other markets already this season, we are working with our shipping partner and insurers to understand the cause and to put additional processes in place to avoid this occurring again."
Te Brake said Zespri was in talks with insurers about the incursion.
"We do have insurance policies in place to cover product contamination but we still have to work through that process with insurers before understanding the full commercial implications. "
RNZ