Number 10 said on Monday that Mr Johnson was aware of rumours about the Tory MP’s conduct but believed all incidents had either been resolved or had not been formally reported.
Mr Pincher is seeking medical help after his resignation from the Government and loss of the Conservative whip over claims that he sexually assaulted two men in the Carlton Club, in central London, last week.
At least 12 other alleged incidents have now been reported in the media. Mark Dabbs, a charity fundraiser in Mr Pincher’s Tamworth constituency, claimed in The Sun on Monday that he had been groped as they posed for a photograph in 2018.
Although it is thought no official complaints have been made to police, Parliament’s independent complaints and grievances scheme is investigating Mr Pincher’s conduct.
Caroline Nokes, the chair of Parliament’s women and equalities committee, said on Monday night that she had encountered Mr Pincher “drunk in the middle of the afternoon” last week.
“I said to a very senior member of the party on the Tuesday ‘there’s a problem there’,” she told TalkTV. “I could smell alcohol on him.
“There’s a culture in Westminster of excessive drinking, and I’m not one of the puritans who says shut down all the bars. I think they have a role to play. But it’s really important that measures are taken when people, when colleagues, have problems.”
Mr Johnson now faces questions over how much he knew about his deputy chief whip’s conduct before he was appointed in a Cabinet reshuffle in February.
His official spokesman said on Monday: “I can’t get into too much detail, but he did take advice on some of the allegations that had been made. But there was no formal complaint at that time and it was deemed not appropriate to stop an appointment simply because of unsubstantiated allegations.
“He was aware that there had been reports and speculation over the years with regards to this individual, but there were no specific allegations.”
The spokesman declined to comment on a claim by Dominic Cummings, Mr Johnson’s former chief adviser, that the Prime Minister had referred to the MP as “Pincher by name, pincher by nature”.
On Monday, Sky News reported that Carrie Johnson objected to Mr Pincher being appointed to the Whips Office while working at CCHQ in 2017. He was later sacked from the role by Theresa May after separate allegations about sexual misconduct.
A Number 10 spokesman told the broadcaster: “Mrs Johnson is a private individual and has no role in ministerial appointments.”
The Telegraph understands that Mr Johnson did not raise rumours about Mr Pincher’s alleged sexual misconduct with him during discussions about a job in the Whips’ Office.
“He relied on the system that exists to sort of give you an objective assessment of that,” a Number 10 source said on Monday night. “That’s what they’re there for.”
Downing Street’s handling of the latest sleaze story has provoked fury on the Tory backbenches, including among recently-elected MPs who feel frustrated at the damage it has inflicted on the Conservative Party.
“I think there is definitely a feeling that yet again they feel let down by the centre. It’s just happening so often that they are getting really p----- off about it,” said one MP from the 2019 intake. “Whatever they do and however much good work they do in their constituency, nothing changes.”
A Government source added that the new intake of MPs had never got to know Mr Pincher because of the pandemic and did not trust him.
“I know that it has gone down worst of all among the backbenches,” the source said. “Especially the new lot, who never liked this person, and found the whole operatic style quite annoying. The theatrics that might have worked in previous years, but over Zoom it’s a bit less scary.”
But other MPs rallied around Mr Johnson and said he was right not to take any action against Mr Pincher until allegations were formally put to the independent complaints and grievances scheme .
“They are just rumours,” one Cabinet minister told The Telegraph. “I know lots of rumours about lots of people. You need allegations, and people to come forward to make complaints.
“In that rumour mill that is Westminster, there are many stories that haven’t come to anything. As soon as the detail was made clear, the Prime Minister acted.”
Another senior Tory MP said: “Rumour is one thing, concrete complaints are another. Chris has now woken up to the reality he has to do something about this. It’s a problem. But there is more than a whiff of this being used as a battering ram to have a go at the PM.”
It is thought Mr Pincher’s resignation has strengthened the resolve of some Tory rebels hoping to change the rules of the 1922 Committee to make it easier to oust Mr Johnson. Any rule change is not expected until at least September.