Pipfruit New Zealand says this year's export apple crop will be down at least 15% on last year.
Chief executive Peter Beaven says growers in both Hawke's Bay and Nelson have had to put up with challenging growing conditions in the past four months.
Although August provided favourable weather for flowering, he says there was a mixture of cold weather, rain and hail in October and November.
The worst affected variety is Braeburn which is expected to drop in production by 30%.
Production of another major export variety, Royal Gala, could be cut by 15%.
Mr Beaven says growers in Hawke's Bay will supply 60% of exports with 31% from Nelson.