"The government has a responsibility to place our vital national interests above highly contested interpretations of international law," he said in his resignation letter to Prime Minister Rishi Sunak, which he posted on X.
"I am unable to take the currently proposed legislation through the Commons as I do not believe it provides us with the best possible chance of success."
The "Safety of Rwanda Bill," published the day after the UK signed a new treaty with Rwanda, is designed to overcome a ruling by the country's Supreme Court that the government's proposed scheme to send thousands of asylum seekers to the east African country was unlawful.
The government said the bill was "the toughest immigration legislation ever introduced" and it would be fast-tracked through parliament.
Immigration minister Robert Jenrick says the government's draft bill "does not go far enough". (EPA PHOTO)
But the proposals are set to cause divisions in Prime Minister Rishi Sunak's governing Conservative Party and could trigger further legal challenges.
"Through this new landmark emergency legislation, we will control our borders, deter people taking perilous journeys across the channel and end the continuous legal challenges filling our courts," Sunak, who has vowed that flights would begin in spring next year, said in a statement.
"We will disapply sections of the Human Rights Act from the key parts of the Bill, specifically in the case of Rwanda, to ensure our plan cannot be stopped."
The bill will instruct judges to ignore some sections of the Human Rights Act (HRA) and "any other provision or rule of domestic law, and any interpretation of international law by the court or tribunal".
Ministers alone would also decide on whether to comply with any injunction from the European Court of Human Rights which issued an interim order blocking the first planned flight last year.
The Rwanda plan is at the centre of Sunak's immigration policy and its success is likely to be key to the fortunes of his Conservative Party, trailing by about 20 points in opinion polls, before an election expected next year and with the issue one of the biggest concerns among voters.
Suella Braverman, sacked from the government last month but who as interior minister had been responsible for immigration, had earlier called for any new law to contain provisions to ignore the European Convention on Human Rights and the HRA.
"The Conservative Party faces electoral oblivion in a matter of months if we introduce yet another bill destined to fail," she told parliament.
Sunak's hardline critics like Braverman have called for the UK to leave the European Convention on Human Rights altogether.
Meanwhile, other Conservatives have warned they might not support a bill which flouts international law.
Legal commentators have said the new legislation would inevitably face challenges in the courts.
The government says the Rwanda scheme would deter migrants from paying people smugglers to ferry them from Europe across the Channel to the UK.
Almost 29,000 people have arrived on the southern English coast without permission this year, after a record 45,755 were detected in 2022.
Meanwhile the cost of housing the 175,000 migrants awaiting an asylum decision is costing 8 million pounds ($A15 million) a day.
In its ruling, the Supreme Court said the plan would violate international human rights laws enshrined in domestic legislation because deficiencies in the Rwanda asylum system meant migrants were at risk of being sent back to their homelands where they were at risk of abuse.
The government said its new binding treaty, which replaced a memorandum of understanding, together with the new law will satisfy those concerns.
"I have been unequivocal that we can no longer tolerate the endless scourge of illegal migration on our country," Sunak said.
"It is costing us billions of pounds and costing innocent lives, and that is why we are taking action to put a stop to it and make clear once and for all that it is parliament that should decide who comes to this country, not criminal gangs."
