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Dover and other Channel ports face disruption for up to six months under a no-deal Brexit, the government has warned.
The warning comes after the government assessed likely traffic flows, if customs checks are delayed.
Although regarded as a worst-case scenario the public sector is being asked to rewrite its contingency plans.
It follows the publication of a hard-hitting report by the county council setting out the impact of a no deal Brexit on key frontline services.
In a letter, the secretary of state for health Matt Hancock, says: "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.”
It continues: “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. In a no deal exit from the EU we would, of course, be pressing member states hard to introduce pragmatic arrangements to ensure the continued full flow of goods which would be to their benefit as well as ours.”
Mr Hancock has written to health leaders, telling them to check their plans for ensuring the continued supply of medicines.
One option is that lorries carrying medicine could get priority at ports and planes used to fly in drugs.
Mr Hancock said: “The Government recognises the vital importance of medicines and medical products and is working to ensure that there is sufficient roll-on, roll-off freight capacity to enable these vital products to continue to move freely in to the UK.
"The Government has also agreed that medicines and medical products will be prioritised on these alternative routes to ensure that the flow of all these products will continue unimpeded after 29 March 2019.”
Meanwhile, KCC says the government should fast track £20 million of funding to help it prepare for possible gridlock on its roads after Brexit.
Cllr Paul Carter, the council’s Conservative leader, said the money was vital to help minimise disruption after next March.