The new trade system with the EU is failing its "first test", it has been claimed, as customs checks and regulations take their toll following the UK's final departure from EU rules at the start of the month.
First Minister Nicola Sturgeon has said the situation is "devastating" for the industry in Scotland.
Reports first emerged last week of new delays and backlogs at ports. Lorries are believed to have even been refused entry at some port locations.
UK ministers warned there was likely to be "significant disruption" at borders over coming weeks.
James Withers, chief executive of Scotland Food and Drink, said on Sunday the situation was now acute.
"More messages from food exporters who are finding the door to the EU is now shut," he tweeted.
"Haulage firms won’t take their loads; bureaucratic/IT systems failing.
"A multi-billion pound trade system is being tested for the 1st time, in real time. And it’s going wrong.
"Brexit, week 1 was bad. Week 2 will be worse."
Mr Withers said the UK Government's dismissal of requests from business organisations for a grace period was a "critical mistake".
He warned this may need to be revisited and said emergency financial aid may also be necessary.
Mr Withers said: "The pain of Brexit this week will be much less visual than many expect. It is unlikely to be the queues of lorries on motorways or on airport runways in Kent.
"It will be the pain of what is NOT happening: cancelled orders and EU customers starting to go elsewhere for their goods."
Much of the Scots food produce exports will only have 24 hours to get to market, but the new delays have been described as "crippling”.
Mr Withers pointed to an 18-step process for moving fish from Scotland to France, adding that firms were given just six hours to prepare for this after the last ditch trade deal agreed in December.
Ms Sturgeon said the situation showed the "real and devastating impact of Brexit on our food exporters”.