The senior Tory said the government had '˜no plans' to use part of the M3 to stack lorries in the event of a no-deal Brexit.
It comes after civic leaders in Hampshire raised fears the motorway would become gridlocked by lorries attempting to get to Portsmouth International Port but wereÂ held up by increased customs checks.
Campaigners fear the tighter security could see up to 500 extra lorries being diverted away from Dover to Portsmouth in a bid to relieveÂ strain on Kent's stretched highway network.
But they say the lorries will have nowhere to go if queues pour out from the port and onto the M275, backing up routes on the M27 and A3(M), and claim a 20-mile stretch of the M3 could be closed to act as a lorry stack.
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However, Mr Grayling has hit back saying this option was not on the cards.
In a letter written by the cabinet minister, and seen by The News, he said the situation faced at Dover was '˜unique' given the '˜exceptionally high volume' of lorries using it and frequent ferry crossings, which could be '˜significantly' affected by delays at border checks.
However, he said: '˜We do not consider there are the same risks at other ports.'
Mr Graying said Highways England had '˜robust contingency plans in place' for a '˜wide range of potential eventualities' after Brexit.
These include '˜routine measures' taken ahead of periods of peak traffic '“ such as the Christmas and summer '“ as well as the ability to respond as unexpected circumstances arise.
Mr Grayling added: '˜Highways England's core task is, and will remain, to keep the road network operating as efficiently and effectively as possible.
'˜We therefore have no plans whatsoever to close the M3 or any other roads outside Kent in a no-deal scenario.
'˜We do not think this would be needed and if there is any disruption there are better ways of dealing with this than by closing strategic roads.'
In the past Kent'sÂ M20 has been closed under the government's Operation Stack initiative, as a way of handling freight traffic queues resulting from disruption to Dover-Calais or Channel Tunnel services.
Stephen Morgan, Portsmouth South MP: '˜Today we've sadly seen yet more chaos from Chris Grayling.
In a matter of days we've seen his department award a contract to a company with no money, no ships, no track record, and no ports, and now he's telling Portsmouth he is ruling out stack arrangements without publishing an assessment, responding to letters or listening to our city.
'˜Under a no-deal, our city faces traffic and congestion chaos. The last thing Portsmouth needs right now is more incompetence. Our city and its businesses need certainty.'
Portsmouth City Council leader, Councillor Gerald Vernon-Jackson added: '˜The government don't seem interested in taking action.'
As previously reported, council chiefs from Portsmouth, Hampshire, Southampton and the Isle of Wight launched a campaign to raise their fears over a no-deal Brexit with the government.
On Monday, Liberal Democrat leader Vince Cable slammed the government for its Brexit negotiations, saying it was '˜amateurish' and '˜Dad's Army-like' during a visit to Portsmouth's port.