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Boris Johnson was aware of "reports and speculation" about the alleged sexual misconduct of the former deputy chief whip, Chris Pincher, before his appointment in February, No 10 says.
Mr Pincher is no longer sitting in Parliament as a Tory MP after a complaint he groped two men.
Since then, he has faced a number of historical claims, which he denies.
Downing Street said Mr Pincher was not blocked from the job because the allegations were unsubstantiated.
Mr Johnson has been under mounting pressure to reveal what he knew about the allegations at the time Mr Pincher was appointed deputy chief whip.
After claims emerged that he had groped two men on Wednesday last week, Mr Pincher resigned as deputy chief whip, telling the prime minister he had drunk "far too much".
On Friday, he was suspended as a Conservative MP, meaning he currently sits in Parliament as an independent.
The prime minister's official spokesman said Mr Johnson knew of "allegations that were either resolved or did not progress to a formal complaint", adding that "it was deemed not appropriate to stop an appointment simply because of unsubstantiated allegations".
The spokesman added that Mr Pincher "had lots of skills and experience for the role", but when asked whether Mr Johnson used the phrase "Pincher by name, pincher by nature", said he would not comment on private conversations.
Education Secretary Nadhim Zahawi said the prime minister has done the "right thing" in his handling of allegations against the MP for Tamworth, in Staffordshire.
Mr Zahawi said "there were of course allegations in the past" but Mr Pincher had denied these and there were investigated and found "not to be correct".
Labour chairwoman Anneliese Dodds has written to the PM seeking details on what No 10 knew of the claims.
"Only Boris Johnson could have looked at this guy's record and thought, 'He deserves a promotion'," she said.
Mr Pincher faces six new claims of inappropriate behaviour stretching back several years, which he has denied.
His resignation last week was the second time he had stepped back from the whips' office, having also quit after Conservative candidate Alex Story accused him in 2017 of making an inappropriate advance.
Mr Pincher was later cleared of any breach of the Conservative Party code of conduct.
On Sunday, Work and Pensions Secretary Therese Coffey said that "to the best of my knowledge" the prime minister had not been aware of specific allegations about Mr Pincher, when he was appointed to the whips' office in February.
She said she had not spoken to the prime minister directly and had received the assurance from the No 10 press office.
What happened when?
Wednesday 29 June: Chris Pincher was seen "extremely drunk" at London's Carlton Club for Conservative Party members, witnesses later told the BBC
Thursday: Mr Pincher resigns as deputy chief whip, telling the PM he "drank far too much", after allegations emerge that he groped two men at the club
Friday: He is suspended as a Conservative MP after being reported to Parliament's behaviour watchdog
Saturday: Mr Pincher says he is seeking professional medical support and is "truly sorry for the upset I caused"
Sunday: New allegations emerge against the MP, which he denies.