The Council of Europe’s human rights watchdog has condemned Rishi Sunak’s Rwanda scheme, saying it raises “major issues about the human rights of asylum seekers and the rule of law”.

The body’s human rights commissioner, Michael O’Flaherty, said the bill, expected to be signed into law on Tuesday after passing its parliamentary stages on Monday night, was a grave concern and should not be used to remove asylum seekers or infringe on judges’ independence.

“I am concerned that the Rwanda bill enables the implementation of a policy of removing people to Rwanda without any prior assessment of their asylum claims by the UK authorities in the majority of cases,” O’Flaherty said, adding that the bill “significantly excludes the ability of UK courts to fully and independently scrutinise the issues brought before them”.

The UK remains a member of the pan-European body that promotes human rights, democracy and the rule of law across the continent.

O’Flaherty warned that the UK was prohibited from subjecting, even indirectly, people to “refoulement” – the act of forcing a refugee or asylum seeker to a country or territory where he or she is likely to face persecution – including under article 3 of the European convention on human rights, under the refugee convention, and under “a range of other international instruments”.

Sunak has said flights will begin taking asylum seekers to Kigali within 10-12 weeks, admitting he would miss his target of flights taking off by spring. Speaking after the passing of the bill, the prime minister pledged it would be a “fundamental change in the global equation on migration”.

But a Home Office minister said the government was prepared for “inevitable” legal challenges to the Rwanda scheme, saying there were those who were “determined to do whatever it takes to try and stop this policy from working”.

Charities and rights groups have condemned the passing of the bill as a “stain on this country’s moral reputation”.

The illegal migration minister, Michael Tomlinson, told Times Radio that the government knew there would be legal battles ahead. “I’m afraid that there will be challenges. There are people who don’t like this policy.”

He said there were “patronising and supercilious” statements about the treatment of gay people in Rwanda, calling it “a very progressive country”.

“Frankly, some of the debate that we’ve heard in the House of Commons and the House of Lords – not recently but in the early days – was very patronising and almost supercilious in looking down at Rwanda,” he said. “So yes, people can be safely sent to Rwanda and it is not unlawful to be gay in Rwanda and discrimination on any grounds is unlawful in Rwanda.”

The bill was passed after a showdown with peers, who eventually conceded on two amendments, but the government is expected to face a number of legal battles as it prepares to deport asylum seekers by July.

The prime minister said the bill was “not just a step forward but a fundamental change in the global equation on migration”.

“We introduced the Rwanda bill to deter vulnerable migrants from making perilous crossings and break the business model of the criminal gangs who exploit them,” he said.

“The passing of this legislation will allow us to do that and make it very clear that if you come here illegally, you will not be able to stay. Our focus is to now get flights off the ground, and I am clear that nothing will stand in our way of doing that and saving lives.”

The deal will cost £1.8m for each of the first 300 deportees, the National Audit Office has confirmed. Earlier on Monday, Sunak had admitted during a press conference that the first flights taking asylum seekers to Kigali would not take off for up to 12 weeks, despite having promised they would do so in the spring.

Lawyers have told the Guardian they will prepare legal challenges on behalf of individual asylum seekers. They can challenge their removal on a case-by-case basis. The Home Office has a list of 350 asylum seekers who are deemed to pose the least risk of submitting successful legal challenges.

The bill allows challenges if a detainee faces a “real, imminent and foreseeable risk of serious irreversible harm if removed to Rwanda”. They must lodge an appeal within eight days of receiving a deportation letter.

Sacha Deshmukh, Amnesty International UK’s chief executive, said the bill “takes a hatchet to international legal protections for some of the most vulnerable people in the world, and it is a matter of national disgrace that our political establishment has let this bill pass.

“The bill is built on a deeply authoritarian notion attacking one of the most basic roles played by the courts – the ability to look at evidence, decide on the facts of a case and apply the law accordingly. It’s absurd that the courts are forced to treat Rwanda as a ‘safe country’ and forbidden from considering all evidence to the contrary.”