"As we near peak harvest, it has become increasingly clear that we will not achieve those initial forecasts," NZAPI chief executive Alan Pollard said.
"Labour availability on orchards and in our post-harvest operations is well short of numbers needed by the industry despite doing all we can to attract New Zealanders into work.
"In addition, the fruit size is coming in smaller on average than we forecast," he said.
The industry now expects the export share of the gross national crop to be around 347,718 tonnes or 19.3 million cartons.
This is 3 million cartons or 14 per cent below 2020, representing a $95-$100 million year-on-year reduction of export earnings.
Of the apple varieties exported, Braeburn was the most significantly impacted with a revised estimate of 1,468,000 cartons - 44 per cent below 2020 levels.
Royal Gala, which remains the variety with the largest share of exports, is now forecast to be 15 per cent or 1,088,000 cartons down on 2020, with Cripps Pink at 15 per cent down and Fuji 19 per cent down.
On the other hand, DazzleTM, EnvyTM, Honeycrisp and RockitTM continue to show strong growth as new plantings come into production, Pollard said.
"While the size profile is smaller than we expected, putting premium sizes into short supply, quality remains very good, and the fruit is well coloured," Pollard said.
"Demand is strong in our key markets, but we remain concerned about continuing disruption to international shipping schedules and port congestion," Pollard said.