Seafood Scotland has claimed the new costs incurred by new customs checks and paperwork are too much for the industry to survive.
Speaking at a Westminster committee on Tuesday, the group’s boss Donna Fordyce warned MPs the sector was facing long-term damage.
She said: "The total time we had before Brexit was 22 hours to get to market. At the moment the best case is 28 [hours, the worst case is 39 hours.
"Customers are finding other supply chains, there's other countries waiting to take up these contracts.
"This will be a long-term loss. How will we regain these markets?"
Delays at the border in January were costing some firms more than £1 million a day, while the new paperwork is expected to cost up to £500,000 a year.
Ms Fordyce has now told MPs the costs will simply be too much for some fishermen.
She said: "I cannot see the new export costs being passed on to the customer and passed back to the fishermen and everybody throughout the supply chain to take their share of between £250,000-£500,000 a year.
"They don't have that profitability to be able to do that.
"So, I think in the medium term we will see a lot more of the smaller companies stopping trade to Europe and it may ultimately be their demise."
Speaking to the Commons environment, food and rural affairs committee, the industry leader claimed calls for a grace period to manage such hits were ignored.
She explained: "We asked for a grace period once we realised what was hurtling towards us.
"Come the start of November we realised that there was going to be issues when we hit January 1, so we wrote a letter to the Prime Minister and asked for that grace period.
"A grace period would hopefully have solved all of these issues. Unfortunately it just didn't happen."
Earlier this year Boris Johnson announced a £23m compensation scheme for firms that can show they suffered a loss, but it is capped at £100,000.