Boris Johnson has suffered a humiliating rebellion over measures to slow the spread of the Omicron variant, with 99 Conservative MPs rejecting plans for vaccine certificates despite surging infections and personal lobbying by the prime minister. Johnson had earlier warned his cabinet of a “huge spike” in cases but failed to convince many in his party to support plans to insist on a Covid certificate or negative lateral flow test to attend large venues. The scale of the rebellion – by far the largest of Johnson’s two-year premiership – raises questions about the prime minister’s willingness to implement tougher restrictions in the coming days, even if these are recommended by the government’s scientific advisers. The vaccine certificates measure passed comfortably by 369 votes to 126 – but only with the backing of Labour. The number of rebels far exceeds Johnson’s parliamentary majority of 79 – and the 56 MPs needed to trigger a vote of no confidence in his leadership. Thirty-five Tory MPs abstained though only 19 were authorised, meaning a further 16 appeared to have refused to vote – a number that included the former prime minister Theresa May. Rebel MPs suggested the final tally voting against could have been 100, suggesting at least one vote had initially been missed. It underlined the prime minister’s increasingly shaky grip over his party, after the damaging Owen Paterson affair and revelations about lockdown-busting parties in Downing Street, which remain under investigation by cabinet secretary Simon Case. After the vote, Keir Starmer called Johnson the “worst possible leader at the worst possible time”. Asked if Tory rebels should try to get rid of the prime minister, the Labour leader replied: “The prime minister needs to ask himself the question whether he has the authority to lead this country through this pandemic.” It was a question some Tories were also contemplating. Geoffrey Clifton-Brown, treasurer of the influential 1922 Committee of backbenchers, said a leadership challenge is “on the cards” if Johnson fails to “change his approach”. As families in Scotland were warned not to socialise in groups of more than three households in the run-up to Christmas, scores of Tories stood up in the House of Commons to slam the significantly less stringent measures being implemented in England. Many MPs raised concerns about the impact of the “plan B” measures on personal liberty and warned that they could lead to tougher curbs on the public’s daily lives in future. Andrea Leadsom, former leader of the House of Commons, said: “This is a slippery slope down which I do not want to slip,” adding that it was “truly appalling” to justify the measures by saying they were less authoritarian than those in other countries. Tim Loughton, another former minister, said: “We cannot head for the hills with kneejerk emergency measures every time a new variant comes along.” New Tory MP Miriam Cates claimed there had been “permanent change to the understanding of what liberty is”. Her colleague Anthony Mangnall urged: “We cannot continue to terrify people.” The backlash against the government’s measures came despite Johnson personally addressing a hastily arranged meeting of the 1922 Committee shortly before the vote. Earlier, England’s chief medical officer, Chris Whitty, had told cabinet that cases of the Omicron variant are continuing to double every two to three days, and would be likely to lead to a “significant increase” in hospitalisations. Whitty said it was too early to say whether cases in South Africa may have plateaued or peaked, as some reports have suggested, and there was not yet reliable evidence about the severity of the variant. Votes on all four plan B measures proposed by the government passed on Tuesday night. There was a more modest rebellion on the reintroduction of mandatory mask-wearing in shops and on public transport, with 40 Conservative MPs voting against. MPs also voted to make vaccinations compulsory for NHS workers, with 61 Conservative MPs voting against – a bigger rebellion than any Johnson had previously faced, though dwarfed by the vaccine certificates result. Labour supported the measure despite having previously objected to mandatory vaccinations for care workers. Keir Starmer suffered his own rebellion on this issue, with 22 Labour MPs voting against, including frontbencher Rachael Maskell, who told the Commons: “I want to win the trust of staff, not push them further away, which this approach will do”. A plan to replace self-isolation with daily testing for contacts of people testing positive for the Omicron variant passed without a division. Downing Street had made concessions in a bid to win over rebels, including allowing a negative lateral flow test to be used as an alternative to proof of vaccination to enter large venues, and promising publicly never to introduce compulsory vaccination. Sajid Javid insisted the measure did not amount to a “vaccine passport”, saying it was “really important to me as a point of principle that people have a range of different routes to show that they are eligible”. The health secretary repeatedly declined to rule out imposing more stringent restrictions, as more data about Omicron emerges in coming days. The shadow health secretary, Wes Streeting, offered staunch support for the government’s measures, with Labour keen to contrast its responsible approach with that of wayward Tory backbenchers. “No matter how dysfunctional the Conservative party has become, the country can rely on Labour,” he told the House of Commons. “We will act in the national interest as we have done throughout the pandemic, putting public health before party politics.” The 99 rebels on Covid certificates dwarfed the 55 who voted against tiered regional restrictions a year ago, in what had previously been the most significant backlash against Johnson’s leadership.