James Withers, chief executive of Scotland Food and Drink, said that even during the height of the pandemic, thousands of boxes a day were being landed at Peterhead fish market in Aberdeenshire -however, this has dwindled significantly since the UK left the EU.
Mr Withers tweeted pictures of the "sad sight" of the fish market hall which lay mostly empty apart from a few crates and said that exporters are being "crippled" by the situation.
It comes after seafood hauliers protested against the Brexit fishing deal by stacking lorries with slogans including “Brexit carnage” and “Incompetent government destroying shellfish industry” near Downing Street on Monday.
In his tweet, Mr Withers wrote: "Europe's biggest fish market in Peterhead like a ghost town. Built to deal with 10,000 boxes/day but with a few hundred.
"Boats tied up, exporters crippled. No Brexit image of lorry queues, it's the sight of trade that isn't moving at all."
Mr Withers told the PA news agency: "Even during the height of the pandemic when a lot of markets were restricted there were still thousands of boxes being landed every day at the market, what this shows is Brexit being a sudden shock to the whole system and export supply chain.
"We warned that systems weren't ready at the end of last year and those warnings weren't heeded, and what has happened is that the EU market, the door to that market has slammed shut for a lot of seafood exporters and that is now having a ripple effect right through the supply chain where fishing boats are tied up in harbour, not out catching, and we're seeing these kind of sparse number of boxes landing on what is normally a market that would be very busy, so it's a real crisis for seafood exporters, fishermen but also other food exporters as well.
"We've spoken to a number of exporters who are concerned that unless this gets fixed very quickly there could be permanent casualties from what is happening."
Prime Minister Boris Johnson confirmed on Monday that any business which experienced difficulty exporting to the EU "through no fault of their own" would be compensated.
Mr Withers said around £750 million worth of Scottish seafood goes to the EU every year and called for political intervention at UK level to sort out the situation.
He said: "The solutions are first for the Prime Minister to deliver on his commitment to compensation but that will only partly heal the immediate financial wounds.
"What we need is urgent dialogue with the European Commission, we need a grace period on these new export checks, which is exactly the grace period that is in place for products coming from the EU to the UK, we need the same for products going in the opposite direction and that will buy us time to fix systems that were completely untested before they went live on January 1, and to see whether we can get a simplified bureaucratic system for exported products.
"There are customers in the EU that want these products and can't get them at the moment. The real risk is that they start going elsewhere for their goods."