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The new measures passed the Commons after support from Labour, but Mr Johnson’s attempts to quell a rebellion on his own backbenches failed as a large number of his MPs defied the Whip to vote against him on the issue of the "vaccine passports".
Sir Geoffrey Clifton-Brown, treasurer of the 1922 Committee, which is the Conservatives' parliamentary group, said a leadership challenge next year has “got to be on the cards” if the PM did not change his approach.
Other measures under the Government’s Plan B also cleared the Commons, but the vote on Covid passes will be seen as a blow to Mr Johnson’s authority after a challenging week.
Earlier, Mr Johnson addressed the 1922 Committee to try to convince them to back his plans.
And he spoke individually to those who publicly said they would oppose the measure earlier in the day.
Some seemed convinced after the meeting, but in the end 126 MPs voted against the use of the passes at nightclubs and large venues.
About 96 Conservative MPs voted against the Covid pass regulations for England. Two Tory MPs also acted as tellers for the no votes.
But 369 MPs backed the move, giving it a majority of 243.
Before Tuesday, the biggest rebellion Mr Johnson had faced was in December 2020, against the strengthening of Covid-19 tier restrictions in England.
Then, 55 Conservative MPs voted against the government. This also includes the two MPs who acted as tellers for the no votes.