The head of the British government's legal department has quit over suggestions that Prime Minister Boris Johnson is threatening to override the Brexit divorce deal with the European Union, the Financial Times said on Tuesday.

The newspaper said Jonathan Jones was leaving his job due to a dispute with Johnson's office over its reported plans to undercut the Withdrawal Agreement treaty signed in January in relation to the Northern Ireland protocol.

The FT said on Monday that Britain was considering tinkering with the deal's special arrangements for Northern Ireland which aim to avoid creating a hard border with the Irish Republic and allow trade to flow while protecting the bloc's internal market.

Britain said in response it was committed to the treaty but that it needed minor clarifications and a backup plan to support the 1998 Northern Ireland peace deal.

Unnamed sources close to Jones, the Treasury lawyer and head of the Government Legal Department, said he was "very unhappy" with the decision to overwrite parts of the Northern Ireland protocol, the FT said.

There was no immediate comment from Johnson's office or from the Cabinet Office.