China has increased inspections of Zespri's kiwifruit after fungus was found in two containers during routine checks.
Zespri was told on Friday the fungus Neofabraea actinidiae was found on four containers at Tianjin Port on 8 June.
The fungus can cause cause fruit to rot in long-term storage.
Zespri said the information it had indicated there was a technical issue and it was working with officials in China and New Zealand.
The Ministry for Primary Industries said it is in talks with Chinese authorities, and exports were continuing.
Two thirds of the 24 million trays of kiwifruit bound for China this season have already been exported.
Chinese officials are reported to have previously warned Zespri there could be retaliation if New Zealand investigated claims of steel dumping.