Rishi Sunak has said the government will appeal against a court ruling that provisions of the UK’s Illegal Migration Act – which created powers to send asylum seekers to Rwanda – should be disapplied in Northern Ireland.

The High Court in Belfast on Monday morning ordered the “disapplication” of sections of the act as they undermine human rights protections guaranteed in the region under post-Brexit arrangements.

The Illegal Migration Act provides new powers for the government to detain and remove asylum seekers it deems to have arrived illegally in the UK. Central to the new laws is the scheme to send asylum seekers to Rwanda.

Mr Justice Humphreys said aspects of the Illegal Migration Act were also incompatible with the European Convention on Human Rights (ECHR), which the UK remains signed up to.

Prime Minister Rishi Sunak said the government would appeal against the ruling and the judgment “changes nothing about our operational plans to send illegal migrants to Rwanda this July or the lawfulness of our Safety of Rwanda Act”.

Following Brexit, the UK and the EU agreed the Windsor Framework, which stipulates there can be no diminution of the rights provisions contained within the Good Friday peace agreement of 1998, even if they differ from the rest of the UK.

The judge found several elements of the Illegal Immigration Act cause a “significant” reduction of the rights enjoyed by asylum seekers in Northern Ireland under the terms of the Good Friday Agreement.

“I have found that there is a relevant diminution of right in each of the areas relied upon by the applicants,” he said.

He added: “The applicants’ primary submission therefore succeeds. Each of the statutory provisions under consideration infringes the protection afforded to RSE (Rights, Safeguards and Equality of Opportunity) in the Belfast/Good Friday Agreement.”

The judge ruled that the sections of the Act that were the subject of the legal challenges should be “disapplied” in Northern Ireland.

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The ruling will fuel a row between Ireland and the UK in recent weeks following the Dublin government introducing plans to return asylum seekers to the UK who cross the border from Northern Ireland into the Republic.

The plans were introduced after the Safety of Rwanda Bill became law at the end of April. The law declares the African nation a safe place to deport asylum seekers to.

Irish justice minister Helen McEntee told a parliamentary committee more than 80% of recent arrivals in Ireland came via the land border with Northern Ireland.

Moday’s cases were brought to Belfast’s High Court by the Northern Ireland Human Rights Commission and a 16-year-old asylum seeker from Iran who arrived in the UK as an unaccompanied child on a small boat from France last summer.

He is currently living in Northern Ireland where his application has not yet been determined but said he would be killed or sent to prison if returned to Iran.

Mr Justice Humphreys agreed to place a temporary stay on the disapplication ruling until another hearing at the end of May, when the applicants will be able to respond to the judgment.

Lawyer Sinead Marmion, who represented the teenager, said the judgment was “hugely significant”.

She said it would prevent the Rwanda scheme applying in Northern Ireland.

“This is a huge thorn in the government’s side and it has completely put a spanner in the works,” she said.

The prime minister said: “This judgment changes nothing about our operational plans to send illegal migrants to Rwanda this July or the lawfulness of our Safety of Rwanda Act.

“I have been consistently clear that the commitments in the Belfast (Good Friday) Agreement should be interpreted as they were always intended, and not expanded to cover issues like illegal migration.

“We will take all steps to defend that position, including through appeal.”

Gavin Robinson, leader of Northern Ireland’s DUP, called on the government to prevent a fracture in immigration policy between the UK’s nations.

He said if nations have different policies it would make Northern Ireland a “magnet for asylum seekers seeking to escape enforcement”.