With the ruling Conservative party deeply divided over Brexit, Johnson said he backed the prime minister but savaged her Brexit policy saying it would leave Britain in a "miserable, permanent limbo".
Former Foreign Secretary Boris Johnson read out a personal statement in Commons earlier in which he took a veiled swipe at Russian Federation, outlined his opposition to Theresa May's Brexit plan, and said "it's not too late to save Brexit".
The Government's defeat on medicines regulation is believed to have been secured by a substantial rebellion by pro-EU Tories.
The MP for Shipley in West Yorkshire said he has "lost trust" in Mrs May's ability to deliver Brexit.
'We never actually turned that vision into a negotiating position in Brussels and we never made it into a negotiating offer, ' he said.
May has risked a leadership contest after the so-called Chequers deal for a post-Brexit Britain that would see the United Kingdom abiding by European Union rules in return for free trade.
Although Varadkar described the no-deal outcome as unlikely, he said preparations were necessary because "we can't make assumptions that the withdrawal agreement will get through Westminster".
In a resignation speech in the Commons, the ex-foreign secretary said a "needless fog of self-doubt" had descended over the past 18 months.
"With eight months until we exit the European Union in March 2019, it is important we all - regulators and industry - continue to plan for a range of scenarios", said Nausicaa Delfas, head of global strategy at the Financial Conduct Authority.
Britain's banks and insurers must plan for a "hard" Brexit in case a transition period is not in place next March, a senior British regulator said on Thursday in a warning echoed by Brussels.
Johnson resigned as foreign secretary last week in protest at the Chequers agreement, which he had initially signed up to.
Former Brexit secretary David Davis called on Mrs May to publish the legal text of a draft free trade treaty based on European Union precedent that was being drawn up while he was still in post, but was stonewalled.
A bristling Mrs May insisted at "absolutely no point" had that happened because "Brexit continues to mean Brexit".
"When I see the dynamics in Westminster, I don't think that there is, at this stage, a majority for whatever type of thing we could ever agree with them", one senior European Union official said.
May also sought to rally support in later meetings with Conservative Party backbenchers known as the 1922 Committee and with the Parliamentary Liaison Committee that includes the leaders of all the House of Commons select committees.
May's win came minutes after an amendment that could have wrecked her Brexit plans was defeated by just six votes.
The government was forced to abandon a plan to start parliament's summer recess five days early, after opponents criticised it as a ploy to avoid further rows, and members of her own party said they still had work to do.