Many fishermen have been unable to export to the EU since catch certificates, health checks and customs declarations were introduced at the start of this year, delaying their deliveries and prompting European buyers to reject them.
Trucks with slogans such as "Brexit carnage" and "incompetent government destroying shellfish industry" parked metres from Johnson's 10 Downing Street office in central London. Police were asking the truck drivers for details.
"We strongly feel the system could potentially collapse," said Gary Hodgson, a director of Venture Seafoods, which exports live and processed crabs and lobsters to the EU.
"Prime Minister Boris Johnson needs to be honest with us, with himself and with the British public about the problems for the industry," he told Reuters. One operator, he said, needed 400 pages of export documentation last week to enter Europe.
David Rosie at DR Collin & Son, which employs 200 people, used to send one or two trucks a night to France carrying live crab, lobster and langoustine worth around 150,000 pounds ($203,000). He said he had not exported a single box this year.
Fishermen, he said, "lost their livelihoods in the turn of a clock" when Britain left the EU's orbit on New Year's Eve.
Under a deal reached last month, British trade with the EU remains free of tariffs and quotas. But the creation of a full customs border means goods must be checked and paperwork filled in, shattering express delivery systems.
Using a phrase that has angered many business owners, Johnson described the changes as "teething problems", and said they had been exacerbated by the COVID-19 pandemic.
Johnson said an additional 23 million pound ($31.24 million) fund had been created to compensate businesses that "through no fault of their own have experienced bureaucratic delays, difficulties getting their goods through where there is a genuine buyer on the other side of the channel".
The government said this extra cash was on top of a 100 million pound investment in the industry over the next few years and nearly 200 million pounds provided to the Scottish government to minimise disruption.
Britain's Department for Environment, Food and Rural Affairs (Defra) said that as well as financial support, it was working with the industry and the EU to address documentation issues.
"Our priority is to ensure that goods can continue to flow smoothly to market," a government spokesperson said in an emailed statement.
Fishing alone contributes 0.1% of Britain's GDP if processing is included, but for coastal communities it is a lifeline and a traditional way of life.
The Scotland Food & Drink association says exporters could be losing more than 1 million pounds in sales a day.
Many in coastal communities voted for Brexit but said they had not expected this impact.
Allan Miller, owner of AM Shellfish in Aberdeen, Scotland, said times for his deliveries of live brown crab, lobster and prawns had doubled from 24 hours. This mean lower prices and some of the product did not survive, he said.
"You're talking 48 hours to 50 hours. It's crazy," he said.
($1 = 0.7383 pounds)
(Reporting by Guy Faulconbridge; Editing by Kate Holton, Timothy Heritage, Jonathan Oatis and Catherine Evans)
By Guy Faulconbridge and Kate Holton