The complaint sparked a disciplinary process that confirmed the MP’s misconduct, BBC News understands.
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, BBC News can reveal.
It triggered a disciplinary process that confirmed the MP’s misconduct.
BBC News understands the PM and the foreign secretary at the time – Dominic Raab – knew about the issue.
The complaint raises fresh questions about what the PM knew before appointing the MP deputy chief whip.
The prime minister’s spokesman said Mr Johnson was aware of media reports and some allegations 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 process concluded, BBC News has been told, but at the time of publication the MP had not responded to our request for comment.
The MP for Tamworth was suspended as a Conservative Party MP last week over allegations he had groped two men at a private members’ club in London.
He quit as Tory deputy chief whip last Thursday, but has since said he was seeking professional medical support and had no intention of resigning as an MP.
In recent days, Mr Pincher has denied a series of new allegations of inappropriate behaviour stretching back several years.
Mr Johnson appointed Mr Pincher as deputy chief whip, which involves ensuring party discipline among Tory MPs, during a cabinet reshuffle in February this year.
Mr Pincher was appointed a Foreign Office minister in July 2019 by Mr Johnson, and stayed in the post until February 2020.
During his tenure as a Foreign Office minister, an official complaint was raised about Mr Pincher for “inappropriate behaviour”.
This 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.”
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.
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”.