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One Teviot Valley orchardist says between 30% and 40% of his crop was damaged because of the sudden torrential Central Otago downpours.
He has also had to lay off staff for the next 10 days.
Other orchards in the valley and Alexandra-Clyde area have fared somewhat better.
The Teviot Valley orchardist, who did not wish to be named, said his first varieties of cherry, Burlat and Earlise, were severely affected by Sunday's downpour.
He said his varieties of cherries came earlier than other pre-Christmas and post-Christmas varieties.
About 30% to 40% of his crop was damaged by 50-60mm of rain, so he had to lay off staff.
''Roxburgh's feeling it at the moment. I employ local people. I feel sorry for them.''
He said the rain did not change the taste of the cherries, but it changed the look.
''The local market won't touch them,'' he said.
He only sells cherries domestically, and understood the impact might have been different for cherry exporters. They usually sold cherries produced later in the season, he said.
Jerry's Cherries owner Jered Tait, of Coal Creek Flat, said he was lucky with the Sunday evening rain, although his early varieties of cherries were affected.
''We have early varieties like Burlat ... but by and large it's not as bad as what we thought,'' he said.
He estimated 10% of his cherries were damaged in the storm.
The rain in Alexandra on Monday night had a minor impact on cherry orchards in Earnscleugh, west of Alexandra.
An Earnscleugh orchardist, who did not wish to be named, said there was only about 6mm-12mm of rain in his orchard and little damage.
H and J Roberts Orchards owner Harry Roberts said he had about 9mm of rain in his orchard which was not a lot but he still had to get helicopters to hover over the area to help dry the cherries, he said.
''Water sitting on cherries reacts differently. The choppers just push air like a big blow drier.''
Mr Roberts said he grew several cherry varieties and the early ones were the worst affected by the storm.
''Maybe 1% was knocked about - the early varieties are in the gun.''