Brandon Lewis, secretary of state for Northern Ireland, in the Commons on Tuesday. He said the legal changes were needed because the government was trying to ‘disapply’ EU law © Parliament TV

Boris Johnson was engulfed in a row with senior figures in his own party and Brussels on Tuesday, after a minister said the government intended to “break international law”.

The admission by cabinet minister Brandon Lewis that the government was going to override an international Brexit treaty with the EU relating to Northern Ireland, astonished Tory MPs and caused alarm in Brussels.

The Financial Times revealed on Tuesday that Jonathan Jones, the head of the government’s legal department, had quit in protest at plans to redraw the Brexit withdrawal agreement. Theresa May, former prime minister, led warnings that the move would damage Britain’s standing in the world.

In response to a question in parliament about the legality of changing the treaty, Mr Lewis, Northern Ireland secretary, replied: “Yes, this does break international law in a specific and limited way.”

More than half a dozen Tory MPs immediately criticised the move, in a sign that Mr Johnson could be facing a serious rebellion. Sir Bob Neill, chair of the Commons justice committee, said “the rule of law is not negotiable”.

Irish foreign minister Simon Coveney reacted angrily to Mr Lewis, saying he had asked the country’s ambassador in London to raise the matter directly with the UK government. 

“There will be no appeasing of this approach,” Mr Coveney told the Irish parliament. “There will be no condoning of a strategy that proposes to breach international law, to undermine an agreement that the EU and the UK signed together less than a year ago.” 

Christophe Hansen, the MEP charged with guiding any EU/UK trade deal through the European parliament, said he feared Mr Johnson’s stance was propelling Britain towards a no-deal outcome.

“This is extremely worrying,” he said. “The UK government is not only gambling with the future of millions of UK and EU citizens by endangering a sensitive peace process in Northern Ireland — it is putting at risk its international credibility at an alarming pace.”

Sterling slipped for a third day on Wednesday, down about 0.3 per cent, dropping below the $1.30 level for the first time since late July. The UK currency lost ground against the euro, too, down 0.2 per cent at €1.099.

The row came as Michel Barnier, EU chief negotiator, arrived in London attempting to unlock stalled trade talks. Asked whether Mr Barnier might head back to Brussels early, an EU official said: “No change as of right now.”

Boris Johnson leaves a cabinet meeting on Tuesday. The PM wants British ministers to have the right to interpret key parts of the Northern Ireland protocol © Simon Dawson/Reuters

Downing Street had initially tried to play down the significance of measures in a new UK internal market bill — to be published on Wednesday — which give British ministers discretion over how to implement parts of the Northern Ireland protocol.

But the resignation of Sir Jonathan lifted the lid on the bitter row at the top of government in which Brexit and the rule of international law came into conflict.

Mrs May spoke for many Tory MPs when she said: “How can the government reassure future international partners that the UK can be trusted to abide by the legal obligations of the agreements it signs?”

Mr Johnson ordered the redrawing of the withdrawal agreement because he wants British ministers to have the right to interpret key parts of the Northern Ireland protocol, a painstakingly drafted legal text designed to avoid a hard border with Ireland.

Mr Lewis explained the legal changes were needed because the government was trying to “disapply” EU law. He added there were “clear precedents for the UK and other countries needing to consider their international obligations as circumstances change”.

Mr Johnson wants to ensure Northern Ireland businesses do not have to fill in export summary declarations when sending goods to Great Britain. He also wants to strictly define the application of EU state-aid rules in Northern Ireland.

Jonathan Jones, head of the UK’s government legal department, has quit over the issue © Paul Heartfield

A planned change to this autumn’s finance bill would allow ministers to determine what sort of goods were “at risk” of travelling into the Republic of Ireland — and liable to EU tariffs when arriving in Northern Ireland from mainland Britain.

Sir Jonathan, permanent secretary at the Government Legal Department, is the sixth senior Whitehall official to resign this year, amid growing tensions between the prime minister and staff at the top of the civil service.

The veteran lawyer was said by colleagues to have been “very unhappy”. Sir Keir Starmer, Labour leader, said: “I know Jonathan. He’s a first-class lawyer. He would not have taken this decision lightly.”

Sir Keir said Sir Jonathan had been overruled by Suella Braverman, the pro-Brexit attorney-general. He said ministers should focus on getting a trade deal rather than “reopening old arguments”.

Tory MP Tobias Ellwood, a former defence minister, said that if Britain broke international law over Brexit, it would weaken its voice when urging China, Russia or Iran to stick to a rules-based order.

“We are all trying to get a trade deal over the line, but in the process we risk losing sight of who we are and the values we uphold,” he said.

Senior figures in the pro-Brexit Conservative European Research Group also expressed their disquiet.

Additional reporting by Arthur Beesley in Dublin

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