The Foreign Secretary dismissed the concerns by saying that drivers who travelled between Camden and Westminster could still easily pay the Congestion Charge.
He insisted it was a “very relevant comparison”.
“There’s no border between Camden and Westminster,” he told BBC Radio 4’s Today programme.
“But when I was mayor of London we anaesthetically and invisibly took hundreds of millions of pounds from the accounts of people travelling between those two boroughs without any need for border checks, whatever.”
Challenged on the comparison, Mr Johnson said: “It’s a very relevant comparison because there’s all sorts of scope for pre-booking, electronic checks, all sorts of things that you can do to obviate the need for a hard border.”
His comments sparked criticism and mockery from other MPs.
Labour’s David Lammy said the intervention “isn’t just stupidity and ignorance but wilful recklessness”.
He added in a jibe at the comparison: “When I was a young boy we were told to stay away from the Troubles on the Caledonian Road and marching bands in Regent’s Park.
“The Chalk Farm Peace Agreement has brought peace in our time. People can get the tube from Camden Town to Finsbury Park without being searched at the border.”
Shadow Northern Ireland secretary Owen Smith called the Foreign Secretary’s comments “typically facile and thoughtless”.
And Chris Leslie, a Labour backbencher and supporter of the pro-EU Open Britain campaign, said: “Now we know why Boris Johnson didn’t mention the problem of the Irish border once in his big Brexit speech last week: because he simply doesn’t understand it.
“Boris Johnson’s tenure as Foreign Secretary and Brexit cheerleader shows he has the reverse Midas touch: everything he touches turns to muck.”
It came amid a damning intervention by the former permanent secretary at the Department for International Trade.
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Martin Donnelly, who resigned last year, compared quitting the single market and customs union to “rejecting a three course meal now in favour of the promise of a packet of crisps later”.
“There is a marked lack of evidence that leaving the EU customs union and single market will lead to greater UK trade with third countries,” a leaked copy of a speech he is due to give on Wednesday said.