Ferry and freight firms will be urged to plan alternative routes for drugs and other vital supplies if a no-deal Brexit blocks cross-Channel traffic.
The suppliers will be told to use Belgian and Dutch ports if blockages at Calais threaten to delay shipments.
The plan emerged after a Cabinet meeting in which ministers were told of contingencies for a no-deal Brexit.
Earlier, MPs were warned that a no-deal could have “catastrophic” consequences for the supply of drugs into the UK.
A senior government source denied there were plans to buy or charter vessels to keep the NHS working.
Instead, private carriers would be expected to carry out their normal roles, the BBC has been told.
But there are worries among ministers and officials that the sudden introduction of border checks at Calais could cause sudden and serious backlogs.
The BBC’s deputy political editor, John Pienaar, said one source described Tuesday’s meeting as “passionate”.
Foreign Secretary Jeremy Hunt was said to have expressed concern that the UK must not be trapped indefinitely in the so-called “backstop” customs union arrangement with the EU, which could hamper the UK from striking wider trade deals.
Attorney General Geoffrey Cox compared that status to being trapped in Dante’s “first circle of hell”.
On Monday, Theresa May told the Commons she too intended any such arrangement to be temporary, and would end “well before” the next election.
Our correspondent says the mood among ministers was more evidence of the prime minister’s limited room for manoeuvre in the Brexit talks, as she prepares to address Tory backbenchers on Wednesday.
Cabinet ministers will receive weekly updates until the UK leaves next March about preparations for Brexit, either with or without a deal.
The government has already asked firms to start stockpiling a six-week supply of drugs and if necessary plan to fly in medicines which cannot be stockpiled due to border delays at sea crossings.
The UK imports 37 million packs of medicine each month from the EU.
Concern has been raised that prolonged disruption at the borders could disrupt the supply chain.
Earlier on Tuesday, Martin Sawer, of the Healthcare Distributors Association, told MPs that the pharmaceutical industry was “very concerned” about a no-deal as it could have “catastrophic” consequences for the supply of drugs.
He warned it could lead to patients being put on drugs that they are not currently prescribed.