Butcher said N.alba was known to be present in many of New Zealand's main trading partners and was not identified by them as a quarantine pest.
"China is fully aware that the rot has been in New Zealand for around 100 years and the vast majority of the apples in the consignments are unaffected and will not cause any biosecurity issues," he said.
"These notifications of the detection of N.alba in themselves are not unusual, as they are part of standard procedures used between trading countries on the interception of a quarantine pest."
New Zealand's apple industry has voluntarily suspended all exports to China for the rest of the season.
Alan Pollard, chief executive of Pipfruit NZ, said the season had "practically finished" so the impact of halting exports would be minimal this year.
But it was "possible" this event could result in China being unwilling to accept New Zealand apples next year, he said.
The MPI, Ministry of Foreign Affairs and Trade, and industry are in discussion with Chinese officials to resolve this issue.
So far this year, New Zealand has exported 320,000 tonnes of apples and 9,500 tonnes of that have gone to China.
"It's a small percentage but it's still an important growth market for us," Pollard said.
The affected apples originated from a small number of production sites and pack houses in Hawke's Bay.
Chinese officials have asked that no apples from those sites be exported to their country.
The Hawke's Bary Today reported that the apple rot was probably a result of heavy rain during harvest. Pacific Queen and Pacific Rose were the varieties most affected, it said.