Philip Hammond warned that the UK will not be able to control key elements of a Brexit no-deal.
The chancellor told BBC Panorama that if the UK leaves without an agreement, the EU will control many of the levers – including what happens in the French port of Calais.
Former Brexit secretary David Davis told the program that Whitehall would never believe that a Brexit would happen without agreement.
The EU has set a deadline of 31 October for the United Kingdom to exit the blockade.
But despite spending 4.2 billion pounds on Brexit preparations, Hammond warned that the government has a limited influence on what a scenario without agreements might look like.
Asked if the United Kingdom can control Brexit, he said: "We cannot because many of the levers are held by others, by the EU 27 or by private companies, we can try to persuade them but we cannot control it".
He added: "For example, we can make sure that the goods flow through the port of Dover without any friction, but we cannot control the flow to the outside in the port of Calais," he told Panorama .
"The French can dial it or dial it, just as the Spanish has been dialing for years or has entered the length of the queues at the border going to Gibraltar."
French officials have previously rejected suggestions of being able to use a "slow-go" policy in Calais if there is no agreement on Brexit – insisting that closing the port would be "economic suicide".
At the beginning of this month, Hammond told parliamentarians that a Brexit without a contract could cost the Treasury up to £ 90 billion and said it would be up to them to ensure that it "didn't happen".
He also said he was "highly unlikely" that he would still be in his job after Theresa May retired next month.
The Panorama program – entitled Great Britain Brexit Crisis – will illustrate tensions in the government during Theresa May's period at number 10 when it is broadcast Thursday.
Mr. Davis, who left Secretary Brexit last year, told the BBC that the Treasury wanted to avoid talking about the prospect of leaving without an agreement.
He concluded that many in Whitehall did not believe it would ever happen, despite two years of planning.
"I have to tell you & # 39; if this doesn't work we'll leave the same & # 39; and you have to believe it.
"And for the fact that you believe it, I have to believe it and I don't think Whitehall ever really believed that they would actually carry out the plans we prepared so carefully for two years."
Leadership favorite Tory Boris Johnson has promised that the UK will leave the EU on October 31st, with or without agreement.
His rival Jeremy Hunt said he could negotiate a new agreement for the United Kingdom "by the end of September" – and "expects" that the UK will leave the EU before Christmas.
Voting among some 160,000 party members is underway, with a winner scheduled to be announced on 23 July.
The British Brexit Crisis is on BBC1 this Thursday, July 18th at 9.00pm.