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Hailstones the size of golfballs and driving rain pelted down on Wednesday afternoon.
The extent of damage from the storm has raised the prospect of higher vegetable prices.
Federated Farmers Arable Industry Group vice chairman Brian Leadley farms near Ashburton, mid-Canterbury, and said peas, sweet corn and potatoes in the early stages of growth have been particularly hard hit.
Mr Leadley told Nine to Noon milling wheat produced for the bread industry had also been damaged.
"A large part of that is into the domestic market, particularly the peas we grow as well as sweet corn and potatoes both domestic and export, I believe have been particularly hard hit.
"Just the stage those potatoes were at; a lot of them had just come up through the ground nice and softly. A lot of that leaf has been stripped off."
Mr Leadley said the extent of the damage would depend on how advanced the crops were in terms of ripening.
On his own property, the pea crop is just one month from harvest, and the storm bruised the plants badly.
"It's just been chopped right off by the hail storm."
Mr Leadley said farmers didn't often buy insurance for crops because it was expensive, though wheat is protected by a compulsory levy paid throughout the industry.
Another farmer estimated that some farmers were facing 20 to 30 percent of their crops affected, though at least some may have suffered damage to half.
"On average that could be $50,000 to $100,000 damage on an average cropping farm, depending on the crop mix."
Yesterday, Federated Farmers South Canterbury Chairman Colin Hurst told RNZ the damage depended on the age and type of crop.
Mr Hurst said the hail had a pretty direct path so only sections of farms were damaged.
Farms closest to Timaru were likely to have been the most badly affected, he said.