Boris Johnson was briefed "in person" about an allegation of Chris Pincher's inappropriate conduct when the MP was a Foreign Office minister in 2019, it has been claimed. 

After days of assurances that the Prime Minister was not aware of any "serious specific allegation", the former permanent secretary at the Foreign Office Lord McDonald said Downing Street made "inaccurate claims". 

Lord Mcdonald, who was the most senior civil servant in the department between 2015 and 2020, wrote in a letter to the parliamentary standards commissioner that Mr Johnson was "briefed in person about the initiation and outcome of the investigation". 

The letter alleges that statements released by No 10 were "not true" and the "modification is still not accurate". 

The claims come after Downing Street confirmed that Mr Johnson knew of concerns about Mr Pincher’s conduct when he made him deputy chief whip in February - but that there were no formal complaints at the time. 

The Prime Minister’s official spokesman said it was not considered appropriate to block the appointment based on “unsubstantiated allegations”.

However, in a letter addressing Kathryn Stone, Lord McDonald wrote: "There was a “formal complaint”.

"Allegations were “resolved” only in the sense that the investigation was completed; Mr Pincher was not exonerated. To characterise the allegations as “unsubstantiated” is therefore wrong."

Deputy Prime Minister Dominic Raab has disputed the claims that Boris Johnson was “briefed directly” about the complaint of inappropriate misconduct. 

Mr Raab, who was foreign secretary at the time, told BBC Radio 4’s Today Programme: “In relation to what happened in 2019, I’m not aware that the Prime Minister was briefed directly about it.

“I have discussed this with the Prime Minister over the last 24 hours, it is not my understanding that he was directly briefed.”

He added: “In relation to the 2019 allegation or complaint, whilst there was inappropriate behaviour, it didn’t trip the wire into disciplinary action.”

The BBC has now reported that both Boris Johnson and then foreign secretary Dominic Raab were made aware of a formal complaint which emerged when Mr Pincher was a minister in the Foreign Office from 2019-20.

On Tuesday, Mr Raab also revealed he had spoken to Mr Pincher when he was a foreign office minister about his conduct and warned him that it must not be repeated.

The Deputy Prime Minister confirmed that Mr Pincher was investigated over a complaint about his conduct at that time but that it wd did not lead to a formal sanction. 

He told Times Radio: “There was a complaint made in October 2019. It was a complaint of inappropriate conduct. I immediately agreed with the permanent secretary he should conduct an assessment whether it warranted disciplinary action.

“He did so. The permanent secretary did not think independently that any formal action under the Civil Service disciplinary processes in the Foreign Office was warranted.

“He spoke to Chris Pincher. I also spoke to Chris Pincher to make sure the behaviour was not repeated.

“I also, for assurance and to make sure we had taken the most rigorous approach, referred the matter to the Cabinet Office ethics and propriety team who looked at it and they confirmed there wasn’t a case for proceeding under the Ministerial Code.

“We followed the processes – I did – to the letter, in fact beyond what was recommended.”

Mr Raab also said that he did not believe there was any reason why Boris Johnson would have been told.

Speaking on the BBC reports, a Government spokesperson said: “There are robust procedures in place for any members of staff to raise allegations of misconduct.

"It is long-standing policy not to comment on any matters involving individual cases.”

The former deputy chief whip Mr Pincher plunged the Government into a new crisis when he quit last week over allegations he groped two men at a Conservative private members’ club.

He had previously resigned from the whips’ office in 2017 over claims he made unwanted advances to a young activist, but was later reinstated after being cleared by an internal Conservative Party investigation.

Over the weekend, however, details emerged in the press of further claims about alleged sexual advances to men – including two fellow Conservative MPs – over a period of years.

Mr Pincher has denied the allegations to the newspapers which carried them.