Heavy rain has destroyed some cherry crops in the biggest growing region, Central Otago.
For the second season in a row, heavy rain has caused cherries to split.
Exports from the region were expected to be 3000 tonnes, worth about $50 million this season, but that figure is now expected to halve.
Summerfruit New Zealand says the ruined cherries from later maturing blocks were only two weeks away from being harvested.
Chairman Gary Bennetts from Roxburgh says some growers now have nothing left to pick.
Mr Bennetts says regions have suffered differing amounts of damage, with Roxburgh getting the most rainfall and then into Alexander and Cromwell.
He says the rain has affected the amount of crop available for market and export.
Mr Bennetts says some growers won't harvest any cherries from some blocks because once the damaged percentage of fruit is too high, it's uneconomic to harvest any.
He says those growers will have to adjust their spending and budget accordingly.
Ruined fruit for the birds
Mr Bennetts says it's uneconomic to process split cherries, so they will be left to the birds.
He says Central Otago apricots have also been damaged by the rain which puts brown markings on the skin so they can't be exported.
Mr Bennetts says that fruit will be sent for processing, which means growers will lose money, but at least recoup some value.