It was not a situation for "blame," he said, for the fungus neofabraea alba, which did not pose a food safety risk and would barely have been detectable at the point of packing.
"It could have started with anything, just a small nick," he said, adding the processes being taken are a "normal part of international trade".
But it's an issue where the risk needs to be minimised as exports of apples to China grow under free trade agreements still in their infancy.
This year there were about 9500 tonnes of apples exported to China, about 2 per cent of New Zealand's total apple export of about 320,000 tonnes worldwide.
Hawke's Bay is the major player, with half the 42 orchards and packhouses on the Apples to China packhouse register being in the region.
Hawke's Bay Fruitgrowers Federation president Leon Stallard said the situation is a case of "working through the processes".
"These things crop up every now and then, so it's a matter of minimising the risk," he said.
It had come at the end of what had been a good season, but not "great" in the context held by some onlookers.
"The indications are the markets have performed very well for us," he said.
"But after 15 years we were due to have a good year ... a year that we've worked damned hard for."
There has not yet been any great impact from the opening of the market to Australia, but Mr Stallard said he believed "meaningful access" could take 10 years or more.
Ministry for Primary Industries import and export plants manager Stephen Butcher said the industry had informed the ministry of the rot detection in China and, considering the season was almost over, had called a voluntary halt on apple exports to China, although the Chinese authorities had asked only that no apples be exported from source sites.
The New Zealand Government and the industry are now working with Chinese quarantine officials to provide technical and scientific information about the offending fungus, and there had been meetings in Beijing.
