Boris Johnson was informed of a formal complaint regarding Chris Pincher's "inappropriate behavior" during his tenure as a Foreign Office minister, BBC News can reveal.
It led to a disciplinary proceeding that confirmed the misconduct of the MP.
BBC News believes that Dominic Raab, the then foreign secretary and PM of the time, knew about the issue.
This complaint raises new questions about the PM's knowledge before appointing MP deputy chief whip.
Monday night, No. 10 stated that the prime minister had not been made aware of any "specific allegations" and that it was inappropriate to suspend the appointment in the absence of a formal complaint.
After the process was concluded, Mr Pincher offered his apology to BBC News. However, the MP did not respond to our request for comment at the time we published the story.
Last week, Tamworth's MP was expelled from the Conservative Party because of allegations that he had groped two men in a London private members club.
Last Thursday, he resigned as Tory deputy chief whip. However, he has since stated that he was seeking medical help and did not intend to resign as an MP.
Recent allegations that Mr Pincher had been engaging in inappropriate behavior over several years have been denied by him.
Mr Johnson appointed Mr Pincher deputy chief whip. This involves maintaining party discipline among Tory MPs during a cabinet reshuffle that took place in February of this year.
In July 2019, Mr Johnson appointed Mr Pincher as Foreign Office Minister. He remained in that position until February 2020.
Pincher was a Foreign Office minister during his tenure. An official complaint was made about Pincher for "inappropriate behavior".
The Cabinet Office supervised the process and produced a report which confirmed misconduct.
The BBC was informed that both the prime minister and the Deputy Prime Minister Dominic Raab were aware of the disciplinary process.
The Foreign Office approached Mr Raab's staff for comment. They said that they had robust measures in place to address any allegations of inappropriate behavior. We have a long-standing policy of not commenting on individual cases.
A spokesman for the prime minister stated that advice was sought from the Cabinet Office's propriety-ethics team before Mr Pincher was appointed deputy chief whip. They did not advise against this move.
A spokesperson for the prime minister said that Johnson was aware of media reports, and some allegations that were not resolved or progressed to a formal complaint.
He said, "It was in some way concluded in some manner." These issues are often anonymous.