Apple rot causing an export ban to China was probably due to heavy rain during harvest, says Pipfruit New Zealand technical manager Mike Butcher.
He said Pacific Queen and Pacific Rose were the varieties particularly affected.
Dr Butcher did not agree with claims by some growers that the drought had contributed to the rot problem - fungicides had not been applied as they were not needed because of the long dry periods.
"These sorts of organisms manifest in storage and are more prevalent in extremely wet harvest periods," he said.
"It requires rain to be released from the capsule that it is in and then the free water running down the tree transports it around."
The rot, caused by the fungus Neofabraea alba, was not a food safety risk but China had indicated it was not present there.
"China undertake a sub-sampling of each consignment and they found evidence on only a few apples, so it is not in every apple, it is not in every box," Dr Butcher said.
Pipfruit New Zealand chief executive Alan Pollard said because China took only 2 per cent of the New Zealand harvest the industry was unaffected at season-end.
Shipments bound for China had been diverted.
"The rot may be a market access problem for China but not in other markets," Mr Pollard said.
He said two pack houses had been identified as being the source of three shipments with the surface rot.
"I don't know how many growers are involved but the number is very small," Mr Pollard said.
The Ministry for Primary Industries had a team in China and they notified New Zealand of the rotten find, he said.
Talks with China about market access for next season will start in February-March.
"This is the nature of international trade. Fruit is designed to rot and sometimes it does."
The rotten apples ban comes while the dairy industry is rebuilding its reputation with Chinese consumers after last month's Fonterra botulism scare.
The New Zealand Infant Formula Exporters Association says New Zealand companies are losing up to $2 million in sales in China each week as a result of the false alarm.