The British team insisted Yates’s departure was not forced by an admission of any kind.
Reports claimed Yates had left his role after an interview with general manager Dave Brailsford, who has stressed there must be a zero-tolerance policy over doping within the team.
A statement from Team Sky read: “Sean Yates, Team Sky’s lead sports director since 2010, has decided to retire from cycling after three decades in the sport.
“After Team Sky reaffirmed its position on anti-doping, the management team started a series of individual interviews with riders, management and support staff.
“Sean has been interviewed and there were no admissions or disclosures that would have required him to leave the team.”