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Boris Johnson on Tuesday faced explosive allegations that Number 10 did not tell the truth over what the UK prime minister knew about inappropriate behaviour by the disgraced former Tory deputy chief whip Chris Pincher.

Lord Simon McDonald, former permanent secretary at the Foreign Office, wrote on Tuesday that Pincher was subject to a formal investigation while a minister in the department in 2019 and that Johnson was told about it.

In a highly damaging letter to the parliamentary standards commissioner, McDonald said Number 10’s original claim that Johnson was not aware of “specific allegations” about Pincher’s behaviour was “not true”.

He added that Number 10’s subsequent explanations about what Johnson knew were “still not accurate”, leaving the prime minister facing renewed accusations that he has not told the truth on a key matter of public concern.

McDonald told the BBC he decided to speak out because Number 10 had had “five full days to get the story correct and that has still not happened”. He said Number 10 appeared to be telling the truth while “crossing their fingers at the same time”.

Pincher resigned as deputy chief whip last week after admitting he had drunk too much at a private members club and had “embarrassed” himself and others. He is accused of groping two men.

Downing Street initially claimed Johnson was not aware of “specific allegations” against Pincher before he was appointed to the whips’ office in February 2022, but Number 10 has been forced to retreat as new evidence emerged.

Dominic Raab, deputy prime minister and former foreign secretary, on Tuesday confirmed that Pincher had been formally investigated while he was a Foreign Office minister for allegedly inappropriate behaviour in the summer of 2019.

McDonald said in his letter that: “An investigation upheld the complaint. Mr Pincher apologised and promised not to repeat the inappropriate behaviour.”

Raab told the BBC it was not clear to him that it was “factually incorrect” that Johnson, who was prime minister at the time, was informed of the investigation or that the complaint against Pincher had been upheld.

Raab said he had discussed the issue with Johnson within the past 24 hours and it was “not my understanding that he was directly briefed”.

But McDonald said a senior government official had briefed Johnson in person. Asked how he was sure, the former mandarin said: “Because that official told me so at the time.”

Downing Street is now under pressure to say which account is correct.

The affair will infuriate ministers who have been repeatedly sent out to defend Johnson with lines that subsequently disintegrate as new evidence emerges or with an incomplete account of what the prime minister knew.

Following allegations that Johnson lied over the “partygate” scandal — a parliamentary inquiry is looking at whether he knowingly misled parliament — the affair will reignite questions over his probity.

Downing Street admitted on Monday that Johnson knew of “allegations that were either resolved or did not progress to a formal complaint”, adding that there were no “substantiated” allegations against Pincher at the time he was made deputy chief whip in February.

McDonald wrote in his letter to Kathryn Stone, parliamentary standards commissioner: “The original Number 10 line is not true and the modification is still not accurate.

“Mr Johnson was briefed in person about the initiation and the outcome of the investigation. There was ‘a formal complaint’.

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

Deputy Labour leader Angela Rayner accused the government of a cover-up, adding: “It is now clear that the prime minister knew about the seriousness of these complaints but decided to promote this man to a senior position in government anyway. He refused to act and then lied about what he knew.”

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