Federated Farmers says there is no doubt China's confidence in New Zealand products has taken a knock.
Apple growers voluntarily halted exports when Chinese officials found three consignments were rotten.
The rot is caused by the fungus neofabraea alba, which has existed in New Zealand for 100 years. It is not a food safety threat but is regarded as a quarantine pest in China.
The discovery of the fungus follows what has already been a tough year for some exporters. New Zealand meat was left stranded on Chinese wharves for weeks over a documentation issue and dairy giant Fonterra only recently emerged from a botulism scare.
Federated Farmers President Bruce Wills says New Zealand has dropped the ball several times and needs to lift its game.
However, Mr Wills also says he feels very optimistic about the long-term trade relationship between the two countries.
"Sadly from time to time mistakes are made, there've been some pretty high profile ones, particularly with China," he says.
"But we've got to learn from those, I think we're going to get on top of this and maintain the position that we've held for a long, long time as a trusted, respected exporter of high quality goods."
New Zealand China Trade Association chairman Tim White says the Chinese market is absolutely critical to New Zealand.
Mr White says some work needs to be done at both Government and industry level to restore China's confidence in New Zealand exports.
This year's pipfruit season is all but over, with just a few containers stilll on the water bound for export markets.