Carrie Johnson openly questioned Chris Pincher’s suitability as a government whip as far back as 2017, Sky News understands.
While communications director at CCHQ in 2017, Mrs Johnson (then Ms Symonds) questioned how Mr Pincher had ever ended up in the whips’ office in correspondence seen by Sky News.
The exchanges followed Mr Pincher’s resignation as assistant whip after claims of unwanted sexual advances from a Tory candidate.
Mr Pincher referred himself to the police and the Conservative Party complaints procedure and was later cleared of wrongdoing.
Theresa May reappointed Mr Pincher to the whips’ office in 2018.
A Number 10 spokesperson said: “Mrs Johnson is a private individual and has no role in ministerial appointments.”
Earlier on Monday, Downing Street confirmed Boris Johnson knew of media reports about the conduct of Mr Pincher when he made him deputy chief whip but felt he could not act on unsubstantiated claims.
The prime minister’s official spokesman said Mr Johnson was “not aware of any specific allegations being looked at” and “in the absence of formal complaint, it was not deemed appropriate to stop an appointment on the basis of unsubstantiated allegations”.
But he said the prime minister was “aware of media reports that others had seen over the years and some allegations that were either resolved or did not progress to a formal complaint”, so sought advice from his propriety and ethics team before the appointment.
Mr Pincher quit the role last week after he was accused of drunkenly groping two men at a private members’ club in London on Wednesday.
The Tory whip was only removed from him on Friday afternoon, meaning he now sits as an independent MP.
Mr Pincher has denied the allegations to the newspapers that carried them.
It was the second time the MP for Tamworth in Staffordshire resigned from the whips’ office, after Conservative candidate Alex Story accused him of making an inappropriate advance in 2017.
Questions have been raised about what the prime minister knew before appointing Mr Pincher in February, with allegations by former chief of staff Dominic Cummings that Mr Johnson referred to the MP as “Pincher by name, pincher by nature” beforehand.
The prime minister’s official spokesperson declined to comment on this claim.
Sir Keir Starmer told Sky News the appointment of Mr Pincher as deputy chief whip was another example of poor judgment by Mr Johnson.
“It’s bad judgment by the PM, a man who puts himself above everyone else – and no, I’m afraid I don’t have any sympathy for him,” the Labour leader told Sky News’ political editor Beth Rigby.
Asked if he would have appointed Mr Pincher if he had been prime minister, Sir Keir replied: “No, I wouldn’t.”
Labour Party chair Anneliese Dodds has written to the PM demanding answers, claiming Mr Johnson is “clearly happy to sweep sexual misconduct under the carpet in order to save his own skin”.
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, Mr Pincher said he would cooperate fully with the inquiry.