Boris Johnson failed to remember he had been told that Chris Pincher was the subject of a official complaint about his conduct, Downing Street has said.

The Prime Minister’s spokesman confirmed that Mr Johnson was briefed on the complaint by officials at the Foreign Office in 2019, a “number of months” after it took place.

The spokesman said the complaint against Mr Pincher – who was Europe minister at the time – was upheld although it did not lead to formal disciplinary action.

No 10 had previously claimed Mr Johnson had not been aware of any “specific allegations”, after Mr Pincher’s dramatic resignation last week as deputy chief whip following claims he groped two men at a private members’ club.

“At the time last week that was the Prime Minister’s view. You will appreciate it takes some time to establish he was briefed, albeit we don’t think in formal briefing on this,” the spokesman said.

“This dates back a number of years. On Friday, it was our belief that he was not informed about that specific incident.”

The admission came after the former top civil servant at the Foreign Office, Lord McDonald, said the original No 10 account was “not true” and the Prime Minister had been briefed “in person”.

In the Commons, responding to a Labour urgent question, Cabinet Office minister Michael Ellis told MPs: “The Prime Minister was made aware of this issue in late 2019, he was told that the permanent secretary had taken the necessary action, no issue therefore arose about (Mr Pincher) remaining as a minister.

“Last week, when fresh allegations arose, the Prime Minister did not immediately recall the conversation in late 2019 about this incident. As soon as he was reminded, the No 10 press office corrected their public lines.”

For Labour, deputy leader Angela Rayner said the latest disclosures revealed an “ethical vacuum” at the heart of Downing Street.

“The Prime Minister was personally informed about these allegations and yet he was either negligent or complicit,” she said.

William Wragg, the Conservative MP who chairs the Commons Public Administration and Constitutional Affairs Committee, said ministers should consider how long they were prepared to carry on supporting the Government.

“I would ask them to consider the common sense of decency that I know the vast, vast majority of them have and ask themselves if they can any longer tolerate being part of a Government which, for better or worse, is widely regarded of having lost its sense of direction,” he told the House.

Since Mr Pincher’s resignation on Thursday, Mr Johnson has been under pressure to say what he knew about his conduct when in February he made him Tory deputy chief whip – a position in which he has responsibility for MPs’ welfare as well as discipline.

Over the weekend a series of reports emerged of allegations over a period of years that Mr Pincher repeatedly made unwanted sexual advances to men.

On Monday, Mr Johnson’s spokesman amended the Government’s line to say that while the Prime Minister had been aware of media reports and speculation, any issues had been resolved and they had not led to formal complaints.

But Lord McDonald said the position was still “not accurate”.

In a letter to the parliamentary standards commissioner he said that a group of officials had complained to him about Mr Pincher’s conduct along similar lines to his alleged behaviour at the Carlton Club.

Following an investigation, the complaint was upheld, Mr Pincher apologised and promised there would be no repeat of his behaviour.

“Mr Johnson was briefed in person about the initiation and outcome of the investigation,” 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.”

Lord McDonald acknowledged that his action was “very unusual” for a retired senior official.

“I did it by myself, because what I have seen and read over the last few days I knew to be wrong. Things get to a point where you have to do the right thing,” he told BBC Radio 4’s Today programme.

In his letter to the commissioner, he said he was acting “out of my duty towards the victims”.

“Mr Pincher deceived me and others in 2019. He cannot be allowed to use the confidentiality of the process three years ago to pursue his predatory behaviour in other contexts,” he wrote.

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

Deputy Prime Minister Dominic Raab, who was foreign secretary at the time, confirmed there had been an investigation into Mr Pincher but that Lord McDonald had advised that it did not warrant formal disciplinary action.

While he said that the then chief whip, Mark Spencer, had been informed, he did not think Mr Johnson had been told, an impression the Prime Minister appeared to confirm when he spoke to him earlier.

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