Foreign secretary Boris Johnson with his Czech counterpart Lubomir Zaorálek. Photograph: Michal Čížek/AFP/Getty Images

Britain is probably leaving the EU customs union, Boris Johnson, the foreign secretary, has claimed, despite Whitehall warnings that it could seriously harm the economy.

The cabinet minister made the revelation in an interview with a Czech newspaper, despite Theresa May’s insistence that her government will not be providing a running commentary on Brexit.

According to the interview, which was reported in Czech, Johnson said: “Probably we will need to leave the customs union, but this is a question which will be dealt with in the negotiations.”

The move is likely to alarm businesses that move goods to and from the EU as it would mean extra checks at the border.

Johnson is also reported to have said that the idea that free movement of people is a founding pillar of the EU is nonsense.

There was some confusion over the colourful language used by Johnson to dismiss the significance of free movement. His phrase was translated by Czech media as “hovadina”, which was then variously translated back again into English as bollocks, rubbish, tosh or bullshit. However, the Foreign Office could not confirm which word he originally used.

“Everybody now has it in their head that every human being has some fundamental God-given right to move wherever they want. It’s not true. That was never the case. That was never a founding principle of the EU. Total myth,” he said.

A leaked cabinet paper revealed by the Guardian last month showed that ministers have been warned that pulling out of the EU customs union could lead to a 4.5% fall in GDP by 2030 and the clogging up of trade through Britain’s ports.

The issue has caused a split among ministers, with Liam Fox, the trade secretary, pushing for the UK to leave because membership of the customs union prevents the negotiation of independent trade deals with non-EU countries.

On the other side, Philip Hammond, the chancellor, and his allies have concerns about the impact of leaving on the economy.

Jonathan Roberts, the head of communications for the UK Chamber of Shipping, said: “Given the huge increase in trade volumes since the customs union was introduced, the reimposition of significant customs checks will have a profoundly negative effect on the shipping industry, as well as both the UK and EU economies.

“If we do leave the customs union, it will be imperative that both UK and EU negotiators create a bespoke deal to allow trade to continue to move freely through our ports. Given the UK’s significant trade deficit with the EU, it is in both sides’ interests to put aside the rhetoric and ideology and create a mutually beneficial arrangement.”

Pressed repeatedly on whether Johnson was right to say the UK would probably leave the customs union, May’s official spokeswoman would only say the foreign secretary was correct that no decision had yet been made. She said Johnson had been engaging with the UK’s partners in Europe by giving an interview to the Czech media outlet.

The foreign secretary, a leading member of the campaign to leave the EU, also continued his attempts to play down concerns about the victory of Donald Trump in the US election.

“There is every reason to be positive. Donald Trump is a dealmaker, he is a guy who believes firmly in values that I believe in too – freedom and democracy. As far as I understand he is in many aspects a liberal guy from New York,” he said.

Ed Miliband, the former Labour leader, said Johnson’s apparently unscripted intervention on the customs union was a sign of the government’s disarray. “With impeccable timing, Boris Johnson now says the UK is ‘probably’ leaving the customs union, thereby proving the Brexit chaos that No 10 is denying,” he said.