Jonathan Jones is the sixth senior Whitehall civil servant to resign this year
Jonathan Jones is the sixth senior Whitehall civil servant to resign this year ©

The head of the UK government’s legal department has quit over Boris Johnson’s proposal to row back on parts of last year’s Brexit deal relating to Northern Ireland.

Jonathan Jones, the Treasury solicitor and 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 Attorney-General’s Office confirmed Sir Jonathan’s departure but declined to comment further. Mr Johnson’s spokesperson said: “We thank him for his years of long service and wish him well for the future.”

Sir Jonathan did not explain his decision in a short resignation letter posted online. But two officials with knowledge of the situation told the Financial Times that he was leaving his position due to a dispute with Downing Street over its plans to challenge parts of the Brexit withdrawal agreement.

Those close to Sir Jonathan said he was “very unhappy” about the decision to overwrite parts of the Northern Ireland protocol, part of the 2019 withdrawal agreement, with new powers in the UK internal market bill.

One person familiar with the events leading up to Sir Jonathan’s decision to resign said it had followed months of tension over the handling of the Brexit negotiations and legal disagreements with Suella Braverman, the attorney-general.

Ms Braverman was appointed in February after the previous attorney-general, Geoffrey Cox, was sacked by Mr Johnson for making what one insider described as “uncomfortable noises” about the importance of abiding by international law. 

Sir Jonathan is understood to have been dissatisfied with Ms Braverman’s initial interpretation of the legal implications of a no-deal Brexit, and requested official advice from government law officers.

Two people familiar with the discussions said questions were raised over whether government plans to override the Brexit withdrawal agreement were in breach of the ministerial code that obliges ministers to follow the law.

In the event, the advice of the law officers was split, with Downing Street deciding to accept the advice of Ms Braverman. 

The government is understood to have commissioned external advice which determined the government, while free to legislate domestically as it saw fit, would be in breach of international obligations if it legislated in contradiction to the withdrawal agreement.

“Jonathan was one of the good guys,” said a person familiar with the internal deliberations. “He’s a man of enormous integrity.”

Number 10 has insisted the new powers were “limited” and were needed to bring clarity to the protocol agreed and signed by Mr Johnson in October last year.

The internal market bill will put powers in the hands of UK ministers to interpret the Northern Ireland protocol. But Michel Barnier, the EU’s chief negotiator, is expected to insist in Brexit negotiations in London on Tuesday that the UK must implement the protocol in full.

Ursula von der Leyen, European Commission president, wrote on Twitter: “I trust the British government to implement the withdrawal agreement, an obligation under international law & prerequisite for any future partnership. 

“The Protocol on Ireland/Northern Ireland is essential to protect peace and stability on the island & integrity of the single market.”

Theresa May, the former prime minister, criticised the government for its proposals in the House of Commons on Tuesday. “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?” she said.

Sir Jonathan became head of the government’s legal department in 2014, having previously worked as a legal adviser and solicitor at the Home Office, the Attorney-General’s Office and the Department for Education. He is also a barrister.

Sir Jonathan’s departure follows the exit of cabinet secretary Mark Sedwill, Simon McDonald from the Foreign Office, Philip Rutnam from the Home Office, Richard Heaton from the Ministry of Justice and Jonathan Slater from the Department for Education.

Dave Penman, head of the FDA union that represents senior civil servants, said Sir Jonathan’s departure was “an extraordinary decision of principle” that represented “the very best values of an impartial and professional civil service”.

“Civil servants, like ministers, have an obligation to uphold the rule of law: the ministerial and civil service code are both unequivocal on this,” he said. “It is, therefore, all the more extraordinary that the government’s most senior legal adviser has decided he has no choice but to resign over an issue that he presumably believes conflicts with his own and ministerial obligations, to act within both the spirit and letter of the law.”

Charlie Falconer, the shadow attorney-general, said “there must be something very rotten about this government” if Sir Jonathan felt the need to resign.

“This resignation indicates that senior government lawyers think that the government are about to break the law,” he said. “The government is trashing the best of the UK: we are a law-abiding country and the government have some serious questions to answer.”

Dominic Cummings, Mr Johnson’s chief adviser, wants civil servants to take more responsibility when policies go awry, but the failure of any minister to quit during the coronavirus crisis has heightened tensions. Mr Cummings has promised radical reform of the civil service, pledging that a “hard rain” will fall across Whitehall.

This article has been amended to remove reference to which government law officers Jonathan Jones sought official advice from.

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