Priti Patel has said the government’s Rwanda migrant policy has not been ruled unlawful after a last-minute intervention by a European court blocked the first deportation flight.

The home secretary told MPs that the injunction was not an “absolute bar” on the removal of the asylum seekers due to have been on the flight – and that they would be tagged while efforts to do so continue.

She insisted that the Home Office would press on with the policy – which has been described as shameful by Church of England and is reported to be regarded as “appalling” by the Prince of Wales – despite legal challenges.

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The Home Secretary accused “the usual suspects” backed by Labour of setting out to “thwart and even campaign against” the government’s efforts and “the will of the British people”.

She added that “mobs” would not be allowed to block removals – an apparent reference to protesters who recently tried to hinder immigration officials from taking a man away in south London a few days ago.

The plane was waiting on a Ministry of Defence runway on Tuesday night when the European Court of Human Rights issued last-minute injunctions to stop the deportation of the migrants onboard.

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English judges in the Court of Appeal had ruled on Monday that the flight could go ahead after a legal challenge by campaigners, who say the government’s plan to send some migrants to the east African country is inhumane.

Ms Patel said the ECHR “did not rule that the policy or relocations were unlawful but they prohibited the removal of three of those on last night’s flight”.

“Those prohibitions last for different time periods but are not an absolute bar on their transfer to Rwanda,” she said.

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“Anyone who’s been ordered to be released by the courts will be tagged while we continue while we progress their relocation.

“While this decision by the Strasbourg court to intervene was disappointing and surprising given the repeated and considered judgments to the contrary in our domestic courts, we remain committed to this policy.”

Yvette Cooper, the shadow home secretary, branded the Rwanda policy a “shambles”.

“This is a shambles and it is shameful and the Home Secretary has no one but herself to blame,” she said.

But Ms Patel said critics had no alternative proposals to deal with “uncontrolled immigration”.

The government argues that its Rwanda scheme will deter migrants from being exploited by people traffickers taking them on the perilous journey across the Channel.

The Home Secretary said: “This government will not be deterred from doing the right thing.

“We will not be put off by the inevitable legal last-minute challenges.

“Nor will we allow mobs to block removals.”

Earlier, Work and Pensions Secretary Therese Coffey told Sky News that the government would appeal the European ruling and was “highly confident” that the next plane chartered under the scheme would take off.

Ms Coffey rowed back from any suggestion that the UK might withdraw from the European Convention on Human Rights, which established the court, saying she was “not aware of any decisions or hints even about that”.

On Tuesday, when asked about pulling out of the convention, Boris Johnson had said it “may very well be” necessary to “change some laws to help us”.

But Tory MPs have voiced their frustration. One of them, Peter Bone, said: “We should withdraw and have our own British convention on human rights.”

Ms Patel told the House of Commons: “It is concerning obviously about the opaque nature in which last night’s appeal was conducted by the European Court of Human Rights, in the way in which they informed the UK government around one individual.

“Of course it is right that we spend time now going back to that court to actually get the grounds upon which they made their decision.”

Downing Street has said the government will do “whatever it takes” to ensure deportation flights to Rwanda go ahead and asked about the withdrawing from the convention said it was keeping “all options on the table”.

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