Boris Johnson was told about an investigation into Chris Pincher's inappropriate behaviour in 2019, despite days of Number 10 saying the prime minister was unaware of specific allegations against his former deputy chief whip.
Mr Pincher resigned his post last week after he was accused of groping two men in a private members club, but it emerged on Monday he had already been investigated for his conduct when working as a foreign office minister three years ago.
In an explosive letter to parliament's standard's commissioner published on Tuesday, former Foreign Office permanent secretary Lord McDonald accused Downing Street of making "inaccurate claims", saying they "keep changing their story and are still not telling the truth".
Speaking to reporters today, a No 10 spokesman confirmed Mr Johnson was briefed on the complaint in late 2019, but said the PM stood by appointing Mr Pincher again in February 2022 as, "at the time when he offered the job, he was not aware of any new specific allegations that were being looked at".
The spokesman also suggested the PM had forgotten he was briefed about the incident, saying: "I would add a caveat at least that this was related to a conversation, and what I believe to have been a brief conversation, that took place around three years ago."
Asking an urgent question in the Commons, Labour's deputy leader Angela Rayner said: "The prime minister was personally informed about these allegations, and yet he was either negligent, or complicit.
"What message does this send about the standards of this government and what they set?"
But Paymaster General Michael Ellis insisted the PM had "acted with probity at all times", adding: "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 [of the briefing], the Number 10 press office corrected their public lines."
When Cabinet Office minister Lord True later repeated the paymaster general's answer to the urgent question in the House of Lords, it was met with laughter from peers - including from those on the government's benches.
Shortly before Lord McDonald's letter was published, Deputy Prime Minister Dominic Raab told Sky News' Kay Burley that he knew about the allegation when he was foreign secretary in 2019.
He said he had "made it clear in no uncertain terms" to Mr Pincher that the behaviour "must never be repeated", and he referred it to both the civil service and Cabinet Office for investigation.
But Mr Raab said the inquiries did not "trigger disciplinary action", and he had only told the PM about the incident "in recent days".
Mr Johnson led a cabinet meeting this morning, letting cameras in for his opening remarks - but not allowing any questions from journalists.
Surrounded by his serious-faced ministers, the prime minister spoke about the cost of living crisis and his plans to tackle it, but there was no mention of Mr Pincher or Lord McDonald's letter.
A number of Conservative MPs criticised their leader over the handling of Mr Pincher, with former chief whip Mark Harper telling Sky News that senior cabinet ministers should consider their positions.
"There are some very good [ministers] who must be feeling very uncomfortable because some of them will be feeling like they've been misled and haven't been given an honest account of what's been going on," he said.
"And if I was them I would be very worried."
His remarks echoed the sentiment of committee chair William Wragg, who accused the government of having "no regard" for upholding standards in public life.
Speaking in the Commons, he asked ministers 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".
Backbench Toy MP John Penrose also questioned when ministers would say "enough is enough".
And the chair of the Liaison Committee - who Mr Johnson will face for a grilling on Wednesday - Sir Bernard Jenkin said promoting people with the "wrong attitudes and the wrong behaviours" gave "permission for the wrong attitudes and the wrong behaviours to persist".
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Mr Pincher resigned as the government's deputy chief whip on Thursday after allegations he drunkenly groped two men at a private members club in London earlier that week.
The party whip was only removed from him - leaving him sitting as an independent MP for his Tamworth constituency - on Friday afternoon after the PM bowed to pressure, and a formal complaint was made to parliament's Independent Complaints and Grievance Scheme (ICGS).
A number of ministers then took to the airwaves to reiterate Number 10's defence of Mr Johnson, including education minister Will Quince, who said on Monday he had been given "categorical assurance" the PM was not aware of any serious specific allegations.
But later in the day, Sky News revealed the PM's wife, Carrie Johnson, also questioned Mr Pincher's suitability as a government whip as far back as 2017.
The deputy leader of the Liberal Democrats, Daisy Cooper, said Lord McDonald had "shone a new light on this murky cover-up".
She added: "Boris Johnson needs to own up to his web of lies and finally come clean today. Every day this carries on our politics gets dragged further through the mud."
And the SNP's Brendan O'Hara called for an investigation into the PM, saying the letter "demolishes Boris Johnson's claims and raises serious questions over whether he has lied and broken the ministerial code".