A “customs partnership”, thought to be favoured by the PM, would involve the UK collecting import tariffs on behalf of the EU.
In a Daily Mail interview, the foreign secretary said it would limit the UK’s ability to do post-Brexit trade deals.
No 10 said the idea was still on the table after ministers failed to agree a customs plan last week.
The newspaper quotes the foreign secretary as saying a customs partnership would create “a whole new web of bureaucracy”.
“If you have a new customs partnership, you have a crazy system whereby you end up collecting tariffs on behalf of the EU at the UK frontier,” he said.
“If the EU decides to impose punitive tariffs on something the UK wants to bring in cheaply there’s nothing you can do.
“That’s not taking back control of your trade policy, it’s not taking back control of your laws, it’s not taking back control of your borders and it’s actually not taking back control of your money either, because tariffs would get paid centrally back to Brussels.”
His comments were made during a trip to the US and he said a trade deal with America could not be achieved if the UK remained “in the lunar pull of Brussels”.
He added that Americans wanted to see “a confident free-trading Britain able to do its own deals”.
At the weekend Mr Johnson’s cabinet colleague Business Secretary Greg Clark said anything other than a close customs arrangement would risk thousands of jobs.
The BBC’s political correspondent Alex Forsyth says the foreign secretary’s comments will stoke tensions in the Conservative party.
The government’s preferred option of a customs partnership has already faced heavy criticism from other Brexiteers – Conservative MP Jacob Rees-Mogg described it as “completely cretinous”.