In some cases, cavity spot has ruined many tonnes of carrots, suffering from low sunlight levels and heavy rain.
MH Poskitt managing director Guy Poskitt, who grows 400ha of carrots in North Humberside, said yields were down by about 15 per cent - around seven tonnes per acre (0.4ha) - as a result of low light levels.
He added: "There has also been one of the worst cases of spot we've ever seen, while early frosts mean open-ground carrots will not fare well. There could be a shortage of good-quality carrots in the spring. We have written off around 10 per cent of our crop."
A further blow came from price hikes, he added. Fertiliser costs had trebled, while electricity bills in the packhouse had jumped 100 per cent in the past year.
Alan Bartlett, managing director of Albert Bartlett & Sons, said yields were down by two to three tonnes per acre across his company's 1,200ha of land for carrots.
"We've just had so much rain, and have had a high amount of cavity spot," said Bartlett, whose firm has bases in Cambridgeshire, Scotland, Lincolnshire and Jersey.
"Next year will depend almost solely on weather. The credit crunch has not affected us. Carrots are a cheaper vegetable: imports and more fancy vegetables will suffer."
Crop consultant David Martin said growers had been "beset by difficult harvesting conditions", which made supplying factories challenging.
"It has led to considerable levels of cavity spot south of Yorkshire," said Martin, who is also vice-chairman of the British Carrot Growers' Association. "Meanwhile, extreme cost inflation with downward price pressure made conditions challenging, with extremely difficult economies and logistics."
He said "modest yields" had been caused by sun levels 20 per cent lower than the norm. Damp conditions would make storage difficult and fungal pathogens more likely, he added.