Ministers will be allowed to block judges from stopping deportation flights in some situations under plans to toughen the illegal migration bill, Sky News understands.

Rishi Sunak has reached a deal with a group of right-wing Tory MPs who had threatened to rebel if the prime minister did not harden the controversial legislation.

It is expected that a new amendment will be introduced allowing ministers to ignore interim injunctions from the European Court of Human Rights that attempt to stop a deportation flight – known as Rule 39 orders.

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Another amendment is expected to say British courts are only able to stop deportations which could cause “serious or irreversible harm”.

A government source told Sky News: “It’s a discretion to opt out on rule 39 orders – still needs final sign off.

“Rule 39 is the interim order used by Strasbourg judges to block the Rwanda flight last year. It is not itself part of the ECHR. It’s a novel legal mechanism.”

Last June, the first deportation flight to Rwanda was grounded following an eleventh-hour intervention by the EHRC, and none have taken off since.

Since then some Tory MPs have been calling for the government to take the UK out of the EHRC altogether to push through tighter border measures.

But those on the more liberal wing of the party want to see more safe and legal routes to stop small boat crossings.

Another government amendment is expected to pledge to draw up plans for safe and legal routes within six months of bill becoming law – to appease MPs on left, a source told Sky News.

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The UNHCR says that the illegal migration bill would breach the UK’s obligations under the Refugee Convention and other laws.

However, a cross-bench peer has suggested the bill risks defeat in the Lords because of the plans to disregard Rule 39 orders.

Lord Thomas of Cwmgiedd, a former Lord Chief Justice said ignoring a ruling would be an “immensely serious step” and “sets an extraordinarily bad example”.

He told BBC Radio 4: “Many people would say having the power to ignore a court order is something – unless the circumstances were quite extraordinary – this is a step a government should never take because it is symbolic of a breach of the rule of law.”

The amendments are expected to be published on Thursday ahead of debates and votes next week.

The illegal migration bill is aimed at changing the law to make it clear people arriving in the UK illegally will not be able to remain in the country.

They will either be sent back to their home country or to a nation like Rwanda with which the UK has a deal, although legal challenges mean no flights carrying migrants have taken off for Kigali.

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But the plan has been shrouded in controversy, with critics including the UN Refugee Agency warning the proposed legislation leaves the UK falling short of its international obligations, and opposition parties dismissing it as unworkable.

However, Conservatives on the right of the party say it does not go far enough.

The compromise comes after Mr Sunak failed to guarantee he could achieve his plan to “stop the boats” by the next election and said it “won’t happen overnight”.

He had pledged to “stop the boats” as one of the five main priorities of his leadership.

But asked in an interview with Conservative Home whether he was confident he could do that by the next election, the prime minister said: “I’ve always said this is not something that is easy; it is a complicated problem where there’s no single, simple solution that will fix it.”