Rishi Sunak is seeking to win over Tory rebels ahead of a crunch vote on his flagship Rwanda plan, after the Prime Minister faced the biggest Conservative revolt of his leadership.

Allies of Mr Sunak have insisted there is only an “inch” between party colleagues, despite two deputy party chairmen quitting to join the ranks of the Tory rebels in the Commons on Tuesday night.

Some 60 Conservatives supported changes to the Safety of Rwanda Bill put forward by Tory veteran Sir Bill Cash, as right-wingers pushed to ensure UK and international law cannot be used to prevent or delay a person being removed to Rwanda.

But the scope of the revolt would be more than enough to sink the legislation and overturn the Government’s working majority if it were repeated at the Bill’s final Commons hurdle expected on Wednesday.

Illegal migration minister Michael Tomlinson sought to play down the depth of Tory divisions in a message to party colleagues, saying: “We all want the same thing.”

“There are disagreements of emphasis. There’s an inch between us, there’s a determination to ensure that the policy works,” he told the BBC.

Chancellor Jeremy Hunt also told broadcasters the party was having a “lively debate” on the matter.

Senior red wall MPs Lee Anderson and Brendan Clarke-Smith resigned from their party positions to vote in favour of changes tabled by Sir Bill and former immigration minister Robert Jenrick.

Jane Stevenson also quit her role as a parliamentary private secretary in the Department for Business and Trade to back the amendments, which MPs on the Tory right say will help protect the Rwanda plan from further legal challenge.

Former prime minister Liz Truss, former ministers Suella Braverman and Sir Simon Clarke and former leader Sir Iain Duncan Smith were also among those to support the changes.

Downing Street is hoping that the vast majority of rebels will not outright oppose the Bill at the next key stage of the parliamentary process, where MPs will vote on the legislation as a whole.

No Conservatives voted against the Bill at second reading – despite similar warnings from the right of the party which had appeared to put it in jeopardy beforehand.

Mr Sunak will also have to face a grilling during Prime Minister’s Questions before the crucial third reading.

Meanwhile, more migrants arrived in the UK on Wednesday as Channel crossings resumed, with groups of people pictured being brought ashore by Border Force in Dover, Kent.

In a sign that Number 10 is looking at fresh concessions to the party’s right wing, Mr Tomlinson confirmed ministers were considering tweaking the Civil Service code to remind officials to follow ministerial decisions.

It comes amid concerns by Tory rebels that the Rwanda legislation fails to go far enough to block last-minute injunctions from the European Court of Human Rights.

The minister did not spell out the exact details, but told BBC Radio 4’s Today programme: “My expectation is that there will be further confirmation that it will be for ministers to decide and then, once those decisions are made, they will be carried out … by our excellent and efficient civil servants.”

But Dave Penman, general secretary of the FDA union which represents senior civil servants, said this would amount to ministers obliging officials to breach the law.

He tweeted: “Code is clear – comply with the law & uphold the administration of justice. Any caveat is a Gov telling its civil servants to break the law – otherwise it wouldn’t be needed.”

Human rights lawyer Adam Wagner said plans to amend the civil service code are “obviously a non-starter”.

“Civil servants can only advise on the basis of the law, and the government’s advice from the Attorney General and (barrister) Sir James Eadie apparently is, rightly, that Rule 39 measures must be complied with in order not to breach the UK’s duties under the European Court of Human Rights.

“So it’s not civil servants who make these decisions, and amending the civil service code won’t make any difference.”

Under the Government’s Rwanda plan, migrants who cross the English Channel on small boats could be sent on a one-way trip to Rwanda rather than being allowed to try to seek asylum in the UK.

The legislation, along with a recently signed treaty with Kigali, is aimed at ensuring the scheme is legally watertight following a Supreme Court ruling against it last year.

The stalled policy comes with a £290 million bill but no asylum seekers arriving via unauthorised routes have been relocated as yet following a series of challenges in the courts.

Several senior Tory figures have threatened to vote down the Bill if it is not changed before its third reading.

Opposition critics accused the Prime Minister of weakness and said the resignations showed that “even senior Tories think that the Conservatives have failed”.

Even if the Rwanda plan does successfully pass the Commons, it is expected to face serious opposition within the House of Lords.