Boris Johnson was made aware of a formal complaint about Chris Pincher's "inappropriate behaviour" while Mr Pincher was a Foreign Office minister from 2019-20.
The complaint led to a disciplinary process which confirmed his misconduct.
BBC News understands the PM and the foreign secretary at the time - Dominic Raab - were told about the complaint.
The claim raises fresh questions about what the PM knew before making Mr Pincher deputy chief whip in February.
For days ministers have insisted Mr Johnson was not aware of specific allegations against Mr Pincher when he was appointed deputy chief whip - whose job it is to uphold discipline among fellow Tory MPs.
Mr Pincher, the MP for Tamworth, was suspended as a Conservative Party MP last week over allegations he groped two men at a private members' club in London. He says he is seeking professional medical support and has no intention of resigning as an MP.
In the latest statement addressing what Mr Johnson knew, Downing Street said the prime minister was aware of media reports and some allegations about Mr Pincher's misconduct that were "either resolved or did not progress to a formal complaint".
He added: "It was in one way concluded in some form. These issues tend to be anonymous."
Mr Pincher apologised after the disciplinary process concluded, BBC News has been told, but the MP has not responded to our request for comment.
The message from No 10 has developed since last Thursday when Mr Pincher first resigned. Since then, Mr Pincher has faced a number of historical claims, which he denies.
On Sunday and Monday morning, ministers continued to stress that Boris Johnson was not aware of specific allegations when he gave Mr Pincher his most recent government job.
But later on Monday, Downing Street conceded the prime minister was previously aware of "reports and speculation", but nothing firmer than that.
The BBC has been told a formal complaint was made against Mr Pincher while he was serving as a Foreign Office minister from July 2019 to February 2020.
An official complaint was raised about Mr Pincher for "inappropriate behaviour" and it triggered a process, overseen by the Cabinet Office, which resulted in a report that confirmed misconduct.
Both the prime minister and Deputy Prime Minister Dominic Raab, the foreign secretary at the time, were made aware of the disciplinary process, the BBC has been told.
Mr Raab's team have been approached for comment, and the Foreign Office said: "We have robust measures in place to respond to any allegations of inappropriate behaviour. It's our long-standing policy not to comment on individual cases."
On Monday evening, No 10 reiterated that the prime minister was not aware of any "specific allegations" being looked at, and that in the "absence of a formal complaint it would not be appropriate to stop the appointment".
Mr Johnson's allies have defended his handling of the situation, with Cabinet minister Jacob Rees-Mogg telling BBC Two's Newsnight: "There's always a lot of gossip going on in politics, there's gossip about all sorts of politicians, an awful lot of which is untrue.
"You can't hire and fire on the basis of rumour... There are rumours about so many people in politics in all parties."
But opposition MPs have been critical, with the Lib Dem MP Daisy Cooper saying: "I think what we've seen time and time again with Boris Johnson is that he's just prepared to carpet over things and try and hope they go away until they become a real problem."
The prime minister's official spokesman has previously said that before Mr Pincher was appointed a deputy chief whip, advice was sought from the government's propriety and ethics team, part of the Cabinet Office, who did not advise against the move.
The spokesman declined to comment on a claim by the PM's former chief aide Dominic Cummings that Mr Johnson had referred to the MP as "Pincher by name, pincher by nature".
"I'm simply not going to comment on content of what was or wasn't said in private conversations," the spokesman said.