The Independent Office for Police Conduct (IOPC) said it is investigating comments Sir Stephen "allegedly made to a Home Office adviser in January 2022".
He is said to have described the bulk of rape complaints as "regretful sex".
Sir Stephen, who was deputy commissioner for the Met at the time, denies making the comments.
The IOPC said the accusations were reported earlier this month, adding both Sir Stephen and the Met had been informed of its decision to investigate.
The IOPC's regional director Mel Palmer said: "The allegation that these comments were made by a very senior police officer is of significant public concern, which may impact on public confidence in policing, and so it is important that they are subject to an independent investigation."
The development comes after a Channel 4 News investigation, in which Prof Betsy Stanko, an adviser appointed by the Home Office, claimed Sir Stephen made the comments at a meeting with top officers.
Prof Stanko had been tasked with conducting Operation Soteria, a report on the way the police responds to rape cases.
She said: "It felt as if he was trying to minimise what the problem was, not taking it seriously.
"He used terms to describe - or a term to describe - what he thought the bulk of the rape complaints were, which was the term 'regretful sex'."
Findings from Operation Soteria declared some officers "displayed a culture of disbelieving victims".
In a statement following the Channel 4 News story, Sir Stephen said: "I categorically deny using the phrase 'regretful sex'.
"These are not words I have ever used in relation to rape or sexual assault, and the reason I am so certain that I did not say this is because I simply do not believe it. I find the phrase abhorrent.
"I find this characterisation of me to be deeply upsetting, and colleagues who know me know how untrue it is."
The watchdog said Sir Stephen resigned as a police officer and is currently employed by the Met as a civilian employee.
The current Met police deputy commissioner, Dame Lynne Owens, referred the matter to the IOPC and said: "Rape is a horrific offence that has a devastating and lasting impact.
"The comments included in the Operation Soteria Bluestone report are wholly unacceptable.
"We recognise that they risk further undermining the confidence of victims to come forward and that is deeply regrettable."
Sir Stephen has held a number of senior positions, including serving as Police Scotland's first chief constable between 2012 and 2015 and being appointed as Acting Commissioner of the Metropolitan Police in April 2022 after Dame Cressida Dick left the position.