Rishi Sunak has survived a damaging row over his flagship Rwanda bill after a Conservative rebellion melted away and dozens of rightwing MPs balked at further undermining the prime minister’s authority. After a crucial 11th hour meeting of more than 45 Tory rebels, the group’s leaders concluded that defeating the bill by voting alongside Labour during an election year could risk collapsing the government. Just 11 Conservative hardliners , including the former home secretary Suella Braverman and Robert Jenrick, the former immigration minister, voted against the legislation, which passed by 320 votes to 276, a majority of 44. There was relief in Downing Street that after days of chaos and infighting at Westminster, during which dozens of Tories rebelled to support amendments to try to toughen up the legislation. Sunak now faces further bruising battles with peers who are already threatening to amend the Rwanda deportation plan in the House of Lords to make sure that it complies with international law. The legislation will then face a series of legal challenges from individuals threatened with deportation to Rwanda. Government lawyers have suggested there is only a “50/50” chance of the first flight taking off before an autumn general election. The Guardian understands that the Home Office has already selected the first 100 people who will be deported. Officials said the cases had been selected because there were no obvious grounds for appeal. Despite his gamble to face down the right of his party paying off, Sunak has been left weakened by the resignations of two Conservative party deputy chairs, Lee Anderson and Brendan Clarke-Smith, and scores of his MPs arguing that the policy will not work. He suffered a further rebellion on Wednesday as 61 Tory MPs voted for an amendment, drafted by Jenrick, that was designed to block last-minute injunctions from European judges. The amendment was ultimately rejected by MPs by 65 to 536. The shadow home secretary, Yvette Cooper, told MPs on Wednesday evening: “This chaos leaves the prime minister’s authority in tatters – he’s in office but not in power. No one agrees with him on his policy. And the real weakness is that he doesn’t even agree with it himself.” At prime minister’s questions, Sunak vowed that he would “get a grip” on the small boats crisis. Yet Downing Street did not deny reports that the Home Office has lost contact with more than 4,000 people earmarked for removal to Rwanda. The government had announced a number of “sweeteners” to make the bill more acceptable to Tory MPs, including a planned change to Whitehall rules meaning civil servants must ignore Strasbourg judgments halting Rwanda deportation flights. However, unions condemned the plans, which mean that Home Office staff removing asylum seekers will be told to implement last-minute injunctions from the European court of human rights only if ordered to do so by a minister. Three civil service unions said this would mean that senior mandarins and border force staff would have to choose between breaking international law, disobeying the instructions of a minister, and resigning. Ministers had already announced plans to expand court capacity and recruit 150 new judges to fast-track asylum appeals under the Rwanda bill. The most senior judge in England and Wales, Sue Carr, spoke out after the announcement, saying the deployment of judges should be “exclusively a matter for the judiciary”. However, ministers were unable to offer the concessions to harden up the bill as a result of warnings from the 100-plus One Nation group of centre-right MPs that they could not tolerate attempts to make the legislation even more hardline. During the second day of debates over the amendments, Jeremy Wright, the former Conservative attorney general, said it would be a mistake for the government to imply that international law does not matter. “What [the government] cannot properly do is set themselves up as judge in their own cause on questions of international law. This house would be wrong to pass a bill that suggested that they could,” he said. In the Commons, Braverman had pleaded with colleagues to vote against the bill, telling them: “This is our last chance to fix this problem. If we get it wrong, the British people will not forgive us.” Tory rebels even drafted their own Rwanda bill, which they said would block all migrant appeals against deportation without breaching international law. A total of 11 Tory MPs voted against the bill, including former cabinet minister Simon Clarke, veteran Tory Bill Cash and New Conservatives leaders Miriam Cates and Danny Kruger. A further 18, from both wings of the party, abstained. However, the majority of Tory rebels came to a different conclusion. “I can’t walk through the voting lobbies with Keir Starmer when there’s an election around the corner and especially on the issue of migration,” one told the Guardian. Others were concerned that blowing up the Rwanda plan by voting against third reading of the bill would immediately throw the government into chaos and leave the Tories facing electoral oblivion. The Tory MP Bob Seely said: “We kill the bill tonight, we can all go and look for new jobs, so that is what we are facing.” Tim Loughton, a former minister, warned Conservative MPs who intended to vote against the bill to “stop and consider before they pull the pin out of another grenade”, arguing that although it was not perfect, it was “the only show in town”. One Tory rebel source, speaking after the last-minute meeting, told reporters: “The majority of those people who spoke in the room have decided to back the bill at third reading. A small number of colleagues will vote no on a point of principle. But the overwhelming likelihood is that the bill will pass probably quite comfortably this evening.” There were farcical moments in a day of drama, as when Rwanda’s president, Paul Kagame, suggested that the UK’s plans to bring in its deportation plan were taking too long. He told the World Economic Forum in Davos: “There are limits for how long this can drag on.” Asked by journalists if he was following the debate in London, Kagame was blunt: “It is the UK’s problem, not ours.” His government has received around £240m from the UK as part of the deal, with a further £50m expected later this year. Kagame suggested this could be returned if Sunak failed to get the deportation scheme off the ground. “The money is going to be used on those people who will come,” he said. “If they don’t come, we can return the money.” However, a Rwandan government spokeswoman later said the country has “no obligation” to return any of the funds paid, but if the UK requested a refund, “we will consider this”. She made clear that this would apply only to a portion of funds that were specifically allocated to pay for support for migrants. Senior Home Office officials have so far refused to say how much more money the UK has already agreed to pay Rwanda under the initial five-year deal. Enver Solomon, the chief executive of the Refugee Council, said the bill would result in thousands of desperate people disappearing in the UK to avoid being deported. “It’s time for the government to admit that the Rwanda plan is entirely unworkable and will only cause more human suffering. “The reality is that the government’s plans are pushing desperate people into unsafe and dangerous situations. We fear many of them will disappear, facing the risk of abuse and exploitation to avoid being sent to Rwanda.”