Ministers have warned of 7,000 long truck queues in Kent after the Brexit transition period ends.
Exporters to the EU face heavy queues and two day delays to trade, the government has warned in a leaked letter.
Imports will also be disrupted in January, according to a letter from cabinet minister Michael Gove to the freight industry.
Gove, responsible for no-deal planning, has written to logistics groups with the Government’s “reasonable worst-case scenario” planning.
He is due to outline the scenario work in the Commons today.
It comes as the European Union’s chief negotiator Michel Barnier prepares to travel to London for further informal talks with his counterpart Lord Frost as efforts continue to strike a post-Brexit trade deal.
The transition period, which kept the UK aligned to the EU’s single market and customs union rules to allow trade to flow smoothly after Brexit, expires at the end of the year unless both sides agree to an extension – something Boris Johnson has ruled out.
The Cabinet Office document states that, in its reasonable worst-case scenario, between 30-50% of trucks crossing the Channel will not be ready for the new regulations coming into force on January 1 2021, while a “lack of capacity to hold unready trucks at French ports” could reduce the flow of traffic across the strait to 60-80% of normal levels.
“This could lead to maximum queues of 7,000 port bound trucks in Kent and associated maximum delays of up to two days,” the documents said.
Such delays could be in place for at least three months, hauliers have been warned, as alternative routes are sought and supply chains get to grips with the new systems and requirements.
In his letter, Gove said: “Irrespective of the outcome of negotiations between the UK and EU, traders will face new customs controls and processes.
“Simply put, if traders, both in the UK and EU, have not completed the right paperwork, their goods will be stopped when entering the EU and disruption will occur.
“It is essential that traders act now and get ready for new formalities.”
But sector chiefs have accused the Government of failing to do enough in recent weeks over the threat of post-Brexit border delays.
Logistics UK, formerly the Freight Transport Association, was seething last week after being told the Government’s Smart Freight system – designed to reduce the risk of cargo delays once Britain is outside of EU rules – would still be in testing mode in January when British exports face new border regulations.
The Road Haulage Association (RHA), meanwhile, said their meeting on Thursday with Gove had fallen “far short of our expectations”.
Responding to the worst-case scenario document, RHA chief executive Richard Burnett said: “We’ve been consistently warning the Government that there will be delays at ports but they’re just not engaging with industry on coming up with solutions.
“Traders need 50,000 more customs intermediaries to handle the mountain of new paperwork after transition but Government support to recruit and train those extra people is woefully inadequate.
“The answers to the questions that we raised in our letter to Mr Gove and subsequent roundtable meeting last Thursday still remain unanswered – and our concern continues to grow.”
A Government spokesman said: “With just 100 days to go until the end of the transition period it’s vital that businesses prepare now for new rules that will come into force at the end of the year, so that they can hit the ground running on January 1 2021 and seize new opportunities.
“As a responsible Government we continue to make extensive preparations for a wide range of scenarios, including the reasonable worst case.
“This is not a forecast or prediction of what will happen but rather a stretching scenario.”