Government’s legal chief quits ‘over Boris Johnson’s plans to unpick Brexit agreement'

Jonathan Jones is said to be ‘very unhappy’ about the controversial move to overwrite the deal

The head of the government’s legal department has quit, apparently in protest at Boris Johnson’s plans to unpick protections for Northern Ireland in the Brexit agreement.

Jonathan Jones is said to be “very unhappy” about the controversial move to overwrite parts of the protocol signed with the EU last year and ratified.

The resignation will fuel criticism that the prime minister is attempting to renege on the agreement – jeopardising peace in Northern Ireland and an EU trade deal.

He is also the sixth senior Whitehall civil servant to resign this year, following the exits of cabinet secretary Mark Sedwill and the permanent secretaries at the Foreign Office, Home Office, Ministry of Justice and Department for Education.

“If he can’t stay in the public service, there must be something very rotten about this government,” said Lord Falconer, Labour’s shadow Attorney General. 

Sir Jonathan’s departure was swiftly followed by the announcement that the director general of the Attorney General’s department Rowena Collins Rice was stepping down, bringing the tally of top mandarins quitting Whitehall to seven.

However, Ms Collins Rice is understood to be moving to a new post in the public sector, in a switch which had been planned for some time.

Downing Street has denied that new legislation – to override requirements for customs checks in the Irish Sea and limits on using state aid – amount to tearing up parts of the Brexit agreement.

It would only be used if talks with the EU failed, it says, but the move does amount to a unilateral act to rework an international agreement, alarming the EU.

Ursula von der Leyen, the president of the European Commission, reminded the prime minister that the Northern Ireland protocol is “an obligation under international law”.

 Sir Jonathan, at a think-tank event earlier this year, made clear it was the job of government lawyers to point out if any action was “incompatible” with ministers’ legal duty.

“Fundamentally, international law is the law. It derives from obligations the government has entered into through treaty or otherwise arise under international law,” he was quoted as saying.

“We treat that as the law, and the government is subject to the rule of law and will comply with those obligations.”

Sir Jonathan is also believed to have clashed with Suella Braverman, the attorney-general and a European Research Group hardliner.

He is understood to have been unhappy with Ms Braverman’s interpretation of the legal implications of a no-deal Brexit, the Financial Times was told. 

The proposed changes to the exit deal will be set out in an Internal Market Bill – to be published on Wednesday – despite the prime minister describing the agreement he ratified as “oven-ready”.

Mr Johnson has also threatened to end the trade talks if there is no agreement by 15 October, while refusing to publish a state aid plan – which is vital to unlock them.

The two chief negotiators, David Frost and Michel Barnier, were opening another round of negotiations in London on Tuesday, but with little apparent hope of a breakthrough. 

The prime minister’s official spokesman refused to discuss the reasons for Sir Jonathan’s resignation, or whether he had signed off the plan to override elements of the withdrawal agreement.

“It is for ministers for determine the legislation which the government puts before parliament,” journalists were told.

On his last day as head of the civil service on Tuesday, former cabinet secretary Sir Mark Sedwill was thanked for his service by the prime minister at cabinet. The national security adviser to two prime ministers, who is the most senior 

The national security adviser to two prime ministers, who is the most senior mandarin to be forced out in Dominic Cummings’s ‘hard rain’ shake-up of Whitehall, was presented with paintings of Queen Elizabeth I’s spymaster Sir Francis Walsingham.