The justice minister stunned No10 by announcing his surprise walk during a speech to a think tank at 9.30am.
Issuing a brutal attack on the PM, Mr Lee said he could no longer support her ill-thought plan as “the UK is not going to be ready in time”.
No10 also fears that other mid-ranking ministers who backed Remain may go before the summer is out, with five names from the mid ranks of the government on a danger list.
One rumoured to be on the verge, business minister Richard Harrington, was yesterday forced to deny the charge publicly.
A leading Tory rebel told The Sun: “I know of at least five ministers who are itching to go because of the mess Brexit has got to.
“It has been terribly mishandled and they feel they can no longer put their names to it.”
Dubbing his decision “a last resort” that had left him “devastated”, Dr Lee insisted: “I would find it hard to live with myself afterwards if I let it pass.”
The practicisng GP insisted he owed his “first responsibility” to his constituents in the Berkshire town of Bracknell – but Leave MPs slammed him after it emerged they voted for Brexit by 54%.
He also called for the government to ask for an extension to Article 50 to delay Brexit until it is properly prepared.
It also emerged yesterday that Dr Lee’s 300-strong local Tory association are now weighing up whether to ditch him as a candidate for the next election.
Chris Boutle, Bracknell Conservative Association chairman, said in a statement the matter was under consideration.
He said: “We note with regret Philip Lee’s decision to resign as a minister at this time and that he is unable to support the Government on a crucial vote this week.
“He has done this as a point of personal principle. He has taken this decision on his own and without consulting the local party beforehand.
“It should be noted that the Bracknell constituency voted to leave the EU in the 2016 referendum.”
It’s understood Dr Lee — who has a personal interest in space issues — was particularly upset over the EU trying to oust the UK from the Galileo programme.
It also emerged that Dr Lee had even failed to tell his own boss, Justice Secretary David Gauke, that he was going.
The stunned PM only received his resignation letter just as she was going into a Cabinet meeting this morning.
The PM’s official spokesman gave a curt response to Mr Lee’s resignation, saying only: “His resignation is a matter for him and we thank him for his service.”
Last night the Daily Telegraph claimed three ministers had discussed joining an anti-Brexit campaign calling for a second EU referendum.
A source said the Best for Britain campaign has held a series of talks with Remain-backing ministers about opposing Theresa May over Brexit.
The move would be a direct challenge to the PM’s authority as she has firmly rejected any suggestion of a second vote on Brexit.
Best for Britain is funded by billionaire George Soros and says it is “working tirelessly” to overturn Brexit.
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