He told BBC Radio 4’s Today programme: “I think it depends how Parliament votes surely - if Parliament was to vote in favour of the deal our Government does then that makes redundant I suspect the referendum. But if Parliament was to reject any deal done by our Government then that opens up clearly what happens then.
“Either our Parliament is sovereign or it is not. If Parliament rejects the deal done by our Government then of course that raises a whole host of questions.
Pressed on whether he would rule out another referendum, the London Mayor repeated that if the Commons rejected a deal brokered by Downing Street with Brussels then it would “open up a whole host of questions”.
The London Mayor, a prominent Remain supporter during last year’s referendum, also said businesses leaders he had spoken to in recent weeks urgently required clarity from the Government on a transition period.
Mr Khan said that two issues “are of the upmost” importance, including the “cast iron” guarantee to EU citizens that their status will not change when Britain formally leaves the bloc in March 2019 and that there will be a transitional period for a “minimum of two years” or possibly longer to ensure stability for businesses.
His comments came after business leaders called for a Brexit transition deal to be agreed “as soon as possible” as firms are preparing to make “serious decisions” with consequences for jobs and investment early in 2018.
The chief executive of Goldman Sachs last week cast further doubt over the banking giant's future in London after Brexit in a provocative tweet.
Lloyd Blankfein said: “Just left Frankfurt. Great meetings, great weather, really enjoyed it. Good, because I'll be spending a lot more time there.”
Mr Khan said: “To be fair to the chief executive of Goldman Sachs, he is articulating publicly what many CEOs, investors and people who love working in London have been saying privately, which is that, unless they have certainty about what happens after March 2019, they have got to make a plan B.”
The Government needed to secure agreement on the plans for a transitional deal as soon as possible otherwise “my fear is other businesses could be thinking about leaving London”, Mr Khan said.
“There are some banks who have already gone public about having to make contingency plans,” he added.
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