The illegal migration minister has rejected suggestions of a deepened split within the Conservative party over the prime minister’s Rwanda bill, saying “there’s a difference of about an inch” between MPs. On Tuesday night, Rishi Sunak faced the biggest rebellion of his leadership after two deputy chairs – Lee Anderson and Brendan Clake-Smith – resigned along with Jane Stevenson, who was Kemi Badenoch’s parliamentary private secretary, by backing rightwing challenges for the prime minister to toughen up his bill. The prime minister’s message to Tory rebels would be a “united one, that actually we all want the same thing”, Michael Tomlinson told LBC. He added: “When we go through the legislation there’s a difference in emphasis, there’s a difference of about an inch … between us in terms of what we want, but in terms of the overall desire and aim, every single Conservative speaker yesterday stood up and said that they want this policy to work.” The chancellor, Jeremy Hunt, also played down the resignations, claiming it was a sign of the “lively debate” within his party. On Wednesday afternoon MPs will vote on the third reading of the Rwanda bill and around a dozen Tories have already said they are prepared to vote against it. Only 29 rebel Tories are needed for the bill to fall. Tomlinson said the bill would get through its third reading and stressed the Rwanda policy would have a “94% deterrent rate”. While he “completely understands the concerns” of his colleagues, as he is the former deputy chairman of the European Research Group (ERG), he hoped “to persuade them that even if there are minor differences in where the emphasis should be”, they were “united and aligned”. In an attempt to move the focus on to Labour, Tomlinson told the BBC Keir Starmer’s party “can’t say what they would do because they are not determined to stop the boats”. Jonathan Gullis has said he is considering rebelling on the legislation, and warned Sunak if the legislation fails, “it will be three strikes and you’re out”. “Everyone agrees in the Conservative party that we must get Rwanda done because it will be a good deterrent factor for people who choose to put thousands of pounds in the hands of smuggling gangs,” the former minister told LBC. “What we need to do is have it as a sustainable deterrent. That means having regular flights with lots of people onboard, otherwise people will just see it as a gimmick, the voters will see it as a gimmick. “We will have tried a third piece of legislation in three years and, if it fails, it will be three strikes and you’re out.” Before the resignations, the lord chancellor and justice secretary, Alex Chalk, announced plans to expand court capacity and recruit new judges to fast-track asylum appeals in an attempt to win over rightwing Tory MPs deciding whether to rebel over the bill. It is understood civil servants may be ordered to obey ministers if they decide to block a European court of human rights order to stop Rwanda deportation flights. The minister confirmed the government is considering tweaking the civil service code to remind officials to follow ministerial directions. “Civil servants advise, ministers decide and then our excellent civil servants carry out those policies,” Tomlinson said. “We are looking at what can be done to strengthen and reassure. But it will be for a minister to make these decisions, not for a court and not for the judges.” But the lady chief justice, Sue Carr, said decisions on how judges were deployed should be “exclusively a matter for the judiciary”, noting the plans outlined by the government to recruit and train 150 judges to help implement Sunak’s Rwanda scheme drew “matters of judicial responsibility into the political arena”.