Downing Street revealed the Prime Minister knew of claims which had been either resolved or not led to a formal complaint, so didn’t feel it was right to block his appointment.
Mr Pincher quit last week after being accused of groping two men in a London club – allegations which prompted a fresh wave of accusations to emerge.
However, Mr Johnson’s spokesman said the Prime Minister had been aware of the “speculation” there had been about Mr Pincher over a number of years when he made him deputy chief whip in February.
The spokesman said: “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 allegation. There was no formal complaint at that time.”
The spokesman also declined to comment on a claim by Mr Johnson’s former chief adviser Dominic Cummings suggesting the Prime Minister had referred to the MP as “Pincher by name, pincher by nature”.
He said: “I’m simply not going to comment on content of what was or wasn’t said in private conversations.”
At the time Mr Pincher was appointed – alongside new chief whip Chris Heaton-Harris – Mr Johnson was facing pressure from Tory MPs seeking to oust him over lockdown parties in Downing Street.
Mr Pincher had previously resigned from the whips office in 2017 over claims he made unwanted advances to a young activist, but was later reinstated after being cleared by an internal Conservative Party investigation.
Earlier junior minister Will Quince declined to deny that he himself had heard rumours about Mr Pincher before last week.
Asked on BBC Radio 4’s Today programme why Mr Johnson appointed Mr Pincher, Mr Quince said: “That is a question and one for the Prime Minister and not for me. I wasn’t in the room and not alive to the conversations.”
He stressed again the former deputy chief whip had been part of the Government largely continuously since 2017, before Mr Johnson’s premiership.
Asked about his own awareness of rumours about Mr Pincher, Mr Quince said: “There are lot of rumours and gossip around Westminster.
"If I had a pound for every rumour that I’d heard about another MP, then I’d be a very wealthy man.”
Mr Pincher now faces an investigation by Parliament’s Independent Complaints and Grievance Scheme after one of the men he allegedly groped last week at the Carlton Club submitted a formal complaint.
In a statement at the weekend, the Tamworth MP, who now sits as an independent, said he would co-operate fully with the inquiry.
He said: “As I told the Prime Minister, I drank far too much on Wednesday night, embarrassing myself and others, and I am truly sorry for the upset I caused.”