Boris Johnson was briefed “in person” about an investigation into the conduct of Chris Pincher when he was a Foreign Office minister, the former permanent secretary at the Foreign Office has said.

Lord McDonald of Salford has submitted a formal complaint to Parliamentary Standards Commissioner Kathryn Stone saying the account given by Downing Street was “not true”.

Earlier, Deputy Prime Minister Dominic Raab confirmed that Mr Pincher – who resigned last week over allegations he groped two men in a private members’ club – had been investigated in October 2019 but said it did not lead to any formal disciplinary action.

He said that while he had informed the then chief whip, Mark Spencer, about the investigation he did not believe it was necessary to tell the Prime Minister.

Downing Street had said that while Mr Johnson was aware of concerns about Mr Pincher when he made him deputy chief whip in February, they had either been resolved or were unsubstantiated.

However, in his letter Lord McDonald said: “Mr Johnson was briefed in person about the initiation and outcome of the investigation. 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”

In his letter, Lord McDonald said that in the summer of 2019, shortly after Mr Pincher was made Europe minister, a group of officials in the Foreign Office had complained to him about his behaviour.

He said that an investigation into the allegations – which were similar to his alleged behaviour at the Carlton Club – had upheld the complaint.

He said Mr Pincher had apologised and promised not to repeat the inappropriate behaviour. There was no repetition at the Foreign Office before he left seven months later to become a housing minister, he added.

Lord McDonald acknowledged that it was unusual to write to the commissioner and simultaneously publicise the letter which he posted on social media.

“I am conscious of the duty owed to the target of an investigation but I act out of of my duty towards the victims. Mr Pincher deceived me and others in 2019,” he wrote.

“He cannot be allowed to use the confidentiality of the process three years ago to pursue his predatory behaviour in other contexts.”

Mr Raab, who was foreign secretary at the time of the complaint against Mr Pincher, offered a sharply differing account of what happened.

He said he asked Lord McDonald to investigate a complaint of “inappropriate conduct” in October 2019.

He said Lord McDonald concluded it did not warrant action under civil service disciplinary procedures, while the Cabinet Office ethics and propriety team said there was no case for proceeding under the ministerial code.

However, he said both he and Lord McDonald spoke to Mr Pincher “in no uncertain terms” about his behaviour.

But while he informed the then-chief whip, Mark Spencer, he did not believe there was any reason why Mr Johnson would have been told.

“I updated and reported back to the chief whip so that he was aware, given the wider responsibility the chief whip has, but I wouldn’t have expected – in relation to something which didn’t merit a formal process, let alone a sanction – to go directly to the Prime Minister,” he told Times Radio.

However, in an interview with BBC Radio 4’s Today programme, Lord McDonald said Mr Johnson was told about the investigation by a senior Cabinet Office official.

“I know that the senior official briefed the Prime Minister in person because that official told me so at the time,” he said.

He said he was not surprised Mr Raab was unaware Mr Johnson was informed.

“That does not surprise me because there are compartments within government,” he said.

“These things are very sensitive, so if there had been the conversation between the Prime Minister and foreign secretary that would be in order, but for there not to be a conversation I can also believe.”