The National Association of Cider Makers has warned its members to prepare for the worst after flooding in the winter devastated almost 17,500 acres of orchards.
The next few weeks will reveal whether the saturation means trees will not blossom.
The NACM has added that the potential crisis could affect crops for the next few years.
Chairman Paul Bartlett told the Bristol Post: “We hope for the best though recognise that the potential impact could seriously affect the income of growers this season and for several years to come.”
The devastation has worried companies such as Bulmers, the world's largest producer of cider, which takes 90 per cent of its apples from local orchards.
Julian Temperley, one of Somerset's most successful growers, said his 170 acres were “touch and go”.
“We've had an appalling late December, January and February - trees over the whole of the South West have taken a hammering,” he added.
“There's certainly a big worry about waterlogged trees - there will be a considerable number dying.
"We have one orchard that's been under a foot of water. I'm not certain if the trees will survive."
The news comes after fruit growers enjoyed a bumper crop last year following a dry winter.