Lorry drivers have been urged not to travel to ports in Kent after France closed its border with the UK for 48 hours.
In a bid to ease congestion in the county, Operation Stack is now in place on the coast-bound M20.
However, speaking to BBC Radio 4, Transport Secretary Grant Shapps said goods were still moving.
“Most of freight is not accompanied and that can still flow of course,” he said.
Late on Sunday night, Mr Shapps asked the public and hauliers not to travel to ports in Kent or other routes to France.
He said he was working urgently with his department “to minimise traffic disruption in the area”.
In Portsmouth, Brittany Ferries said it was unable to carry passengers and accompanied freight vehicles to Caen as expected.
It said the border closure would affect around 1,000 passengers and 400 freight vehicles planning travel to France on Monday and Tuesday.
Operation Stack is an emergency measure designed to prevent gridlock in Kent. Police work with Highways England and the county council to put it in place.
Under the measure, freight is separated into two queues on either side of the coast-bound carriageway between junctions 8 and 9.
One lane is used for traffic heading to the Eurotunnel terminal and one lane is for port traffic. The middle lanes are kept clear for emergency vehicles.
Non-freight traffic is diverted off the motorway and onto the A20.
About 10,000 lorries a day travel between Dover and Calais during peak periods such as Christmas.
But the decision by France to close its borders means no accompanied freight (being transported by a driver) can leave and long queues are expected.
The leader of Kent County Council, Roger Gough, said: “National government has urged vehicles not to come to Kent because we are anticipating some 17,000 vehicles coming into the county to make the crossing over the next couple of days.”
Manston Airport in Kent is being prepared to take up to 4,000 lorries, the Department for Transport has confirmed.
Lorry driver Rick Mayo, who is stuck at Medway Services, told the BBC he thought the situation was “ridiculous”.
He said: “Truck drivers don’t come into contact with people, we’re in the truck on our own, we self-isolate for three or four days at a time.
“Then, when we do [come into contact with other people], it’s limited with masks and with gloves on”.
There are fears the border closure could disrupt food supplies and cause difficulties meeting orders for British goods in continental Europe.
The chief executive of the Road Haulage Association, Richard Burnett, said the “fresh food supply where it’s short shelf life and there will be product on its way now, that’s where the challenge comes from”.
But Mr Shapps said: “The shops are well stocked. In the short term this is not an issue in terms of supply but we are very keen to get it resolved.”