The head of the Government Legal Department has resigned amid anger over suggestions Boris Johnson is planning to override elements of the Brexit Withdrawal Agreement.

Sir Jonathan Jones’s departure was confirmed by the Attorney General’s Office, which declined to comment on the reason for the latest exit in a string of resignations of top civil servants.

The Financial Times reported on Tuesday that Sir Jonathan was quitting as the department’s permanent secretary due to a dispute with Downing Street.

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Prime Minister Boris Johnson Prime Minister Boris Johnson (Stefan Rouseau/PA)

Two Whitehall officials were said to have told the paper that he was departing over concerns the Prime Minister wanted to row back on parts of the Brexit deal relating to Northern Ireland.

A spokesman for the Attorney General’s Office said: “I can confirm Sir Jonathan has resigned but cannot comment further.”

His is the sixth resignation of a senior civil servant this year amid growing tensions between officials and Downing Street as Mr Johnson and his top aide Dominic Cummings plan an overhaul of Whitehall.

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Labour’s shadow attorney general Lord Falconer tweeted: “Jonathan Jones impressive lawyer and very decent person. Loyal civil servant.

“If he can’t stay in the public service, there must be something very rotten about this Government. Reckless, law breaking, trashing the best of the UK.”