The American businessman reportedly told a technology conference in Boston two weeks ago that he would have thought twice about building a European headquarters in London had he known the UK was going to quit the EU.
"Maybe I wouldn't have" opened the £1bn City office, he said.
"My former wife was a Brit, my daughters have British passports, so we love England - it's the father of our country, I suppose," Mr Bloomberg said, according to The Guardian.
"But what they are doing is not good and there is no easy way to get out of it because if they don't pay a penalty, everyone else would drop out.
“So they can't get as good of a deal as they had before."
He added: "I did say that I thought it was the single stupidest thing any country has ever done but then we Trumped it."
It comes after the City called for clarity over plans for a post-Brexit transition period by the end of the year.
The City of London Corporation warned Chancellor Philip Hammond it was "critical" details were set out quickly or contingency plans will be put into force.
Additional reporting by PA
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