Top government lawyer quits over Boris Johnson’s proposed changes to the Brexit Withdrawal Agreement

Sir Jonathan Jones is the sixth Whitehall official to resign this year amid growing tensions between Downing Street and the civil service, the FT has revealed.

Two insiders with knowledge of the matter told the paper that Jones, who is the Treasury solicitor and permanent secretary of the Government Legal Department, was stepping down after discovering Downing Street plans’ to overwrite key aspects of the Northern Ireland Protocol.

Jones is said to be ‘very unhappy’ about the decision to add new powers into the UK internal market bill that would effectively legislate against the Withdrawal Agreement.

Number 10 has insisted the new powers were ‘limited’ and were necessary needed to bring clarity to the protocol agreed and signed by Johnson last October.

Proposed changes to the internal market bill will allow government ministers to interpret the Northern Ireland Protocol.

Chief EU negotiator Michel Barnier has threatened to pull the latest round of Brexit trade talks in London if Britain reneges on its responsibilities under the Withdrawal Agreement.

Usula von der Leyen, European Commission president, tweeted: ‘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.’

Liberal Democrat Brexit spokesperson Christine Jardine said: ‘The head of the government’s legal department quitting over Boris Johnson’s approach to Brexit should signal how serious a situation this is.

‘For Johnson to think it is acceptable to row back on international agreements and assurances made to Northern Ireland shows he has no respect for international law or the UK’s obligations.

‘How can the UK expect other countries, like China, to respect the international treaties we hold with them if we don’t do the same when it comes to the Withdrawal Agreement?

She added: ‘Any government figure of any integrity would be appalled at these plans. It is therefore unsurprising that Sir Jonathan has felt the need to leave his position.’

Jones became head of the government’s legal department in 2014 following stints at the Home Office, the Attorney General’s Office and the Department for Education.

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.

The Cabinet Office has declined to comment.