Carrie Johnson is said to have openly questioned Chris Pincher's suitability as a Government whip back five years ago, according to reports.
The then-communications director of the Conservative Party was said to have sent messages asking how the MP ended up in the whips' office.
The exchanges, Sky News say they have seen, came after he resigned as a whip in 2017 following claims of unwanted sexual advances to a Tory candidate.
Mr Pincher referred himself to the police. He was later cleared of any wrongdoing by an internal Tory investigation and reappointed by Theresa May.
The incident took place before Mrs Johnson, then Carrie Symonds, began her relationship with the married Foreign Secretary.
A Number 10 spokesperson said: "Mrs Johnson is a private individual and has no role in ministerial appointments."
Brexit opportunities minister Jacob Rees-Mogg said “you can’t judge people on rumours” when asked whether it was appropriate for the PM to make Chris Pincher deputy chief whip despite claims about his conduct.
He told LBC’s Tonight With Andrew Marr: “There were rumours.
"I think prime ministers have to be just, they can’t just say, ‘I’ve heard a bit of gossip and I think you’ve done something that I wouldn’t approve of’."
Labour leader Keir Starmer has said Mr Pincher's appointment was another example of poor judgment by Boris Johnson.
Speaking during a round of broadcast interviews, Sir Keir told Sky News: “I have got no sympathy with a Prime Minister who repeatedly makes bad judgment calls.
“We have been living with a version of this story for month after month after month. Bad judgment by a man who puts himself above everything. I don’t have any sympathy for him.”
It comes after Downing Street confirmed Boris Johnson was aware of concerns about the conduct of Chris Pincher when he made him deputy chief whip.
The Prime Minister’s official spokesman said the while he knew of claims which had been either been resolved or had not resulted in a formal complaint, it was not considered appropriate to block his appointment.
No 10 – and a succession of ministers – had previously stated that Mr Johnson had not been aware of any “specific allegations” against Mr Pincher.
Mr Pincher plunged the Government into a new crisis when he dramatically quit last week over allegations he groped two men at a Conservative private members’ club.
He 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.
