A no-deal Brexit could lead to six months of chaos on key cross-Channel routes, according to the latest Government assessment.
Ferries between Dover and Calais and traffic using the Channel Tunnel could be disrupted until the end of September 2019.
A letter sent by Health Secretary Matt Hancock to the pharmaceutical industry and NHS contained the warning.
He said: "Although we cannot know exactly what each member state will do with respect to checks on the EU border, the cross-Government planning assumptions have been revised so we can prepare for the potential impacts that the imposition of third country controls by member states could have.
"These impacts are likely to be felt mostly on the short straits crossings into Dover and Folkestone, where the frequent and closed loop nature of these mean that both exports and imports would be affected.
"The revised cross-Government planning assumptions show that there will be significantly reduced access across the short straits, for up to six months.
"This is very much a worst-case scenario; however, as a responsible Government, we have a duty to plan for all scenarios. "
Ministers are drawing up plans to fly in vital drugs and give priority to lorries carrying medical supplies at gridlocked ports.
Paul Carter on Brexit planning for #Kent: "I hope we never have to implement any of our contingency plans and the UK has a smooth exit from Europe."However, we don't know whether or not that will be the case." https://t.co/K0nGdCcZwJpic.twitter.com/kbtEFpollH
— KCC Communications Office (@KCCpressdesk) December 7, 2018
Kent Council's leader Paul Carter called for emergency measures to prevent lorries entering the county to avoid chaos on the roads.
"We now need far more input and information from national Government in how they are going to work with us," he said.
"There must be a national freight transport plan which, when necessary, can hold lorries back from coming into Kent in the first place should the need arise."
With the Commons vote on Theresa May's Withdrawal Agreement expected to result in it being rejected by MPs, the risk of a no-deal Brexit could increase.
Former foreign secretary Boris Johnson said the Brexit deal obtained from Brussels by Mrs May is similar to the conditions that might be imposed on the defeated side in a war.
As the Prime Minister sent senior colleagues out around the country to sell her deal, Mr Johnson repeated his call for MPs to throw it out in the Commons vote next Tuesday.
The Prime Minister was coming under growing pressure to delay the December 11 vote to give herself time to ask for more concessions from the EU at a Brussels summit at the end of next week.
With three days of the five-day debate complete, Press Association analysis showed that of 163 MPs who have spoken, just 27 have indicated they will back Mrs May's deal compared to 122 – including 29 Tories – who will vote against.
Latest numbers:– 163 MPs have now spoken in the Brexit debate– 122 indicated they will vote against the deal, including 29 Conservatives– 27 will vote in favour– 14 are undecided
— Ian Jones (@ian_a_jones) December 7, 2018
Senior Conservative MP Sir Graham Brady, chairman of the backbench 1922 Committee, said he would welcome deferring the vote to allow time to settle the question of how the UK removes itself from the so-called "backstop" arrangements for Northern Ireland.
However, a spokesman for Mrs May insisted the vote would be held on Tuesday.
There are many exquisite humiliations in the so-called "deal" with the EU that parliament is being asked to endorse on...
Writing on Facebook, Mr Johnson said that the backstop "hands the EU the indefinite power to bully and blackmail this country to get whatever it wants in the future negotiations", because it denies the UK the power to leave without agreement from Brussels.
Predicting that France will use this advantage to "plunder" UK fishing waters, Spain will "make another push for Gibraltar" and Germany will demand concessions on migration, the former foreign secretary said: "It is quite incredible that any government could agree to such terms.
"They resemble the kind of diktat that might be imposed on a nation that has suffered a military defeat."
The Border Delivery Group, a Whitehall co-ordination group for Government departments that have an interest in border issues, was holding discussions with key stakeholders on Friday, a spokesman for Mrs May said.
The discussions centre on "the Government's no deal planning assumptions for the border", the spokesman said.
Labour leader Jeremy Corbyn said that "all options" – including a second referendum – must be on the table if Mrs May goes down to defeat next week.
Writing in The Guardian, Mr Corbyn made clear that his preferred result remains a general election which might allow Labour to try to secure a Brexit involving a customs union which gave the UK a say in future EU trade deals, as well as a new single market deal allowing Britain control over migration and state aid.
"In the past, a defeat of such seriousness as May now faces would have meant an automatic election," said the Labour leader.
"But if under the current rules we cannot get an election, all options must be on the table. Those should include Labour's alternative and, as our conference decided in September, the option of campaigning for a public vote to break the deadlock."
Conservative chairman Brandon Lewis said it was "the strongest signal yet that Labour are considering backing a second referendum, breaking his promise to respect the country's decision to leave".
Foreign Secretary Jeremy Hunt warned of "real social instability" if a second referendum resulted in a victory for Remain.
"For me as someone who voted Remain, my view is we will not have social stability in this country if we end with a solution that doesn't mean that we have parliamentary control of immigration policy," he told The Times Red Box.
If a fresh poll reversed the 52%-48% majority for Leave in 2016, Leave supporters "would be incredibly angry and I wouldn't rule out real social instability in this country", he said.
Meanwhile leaked Government papers obtained by The Times suggested that Ireland could suffer more from a no-deal Brexit than the UK, with a projected 7% drop in GDP compared to 5% for Britain.