"After a long career in professional cycling, he has told us that he wants to move on, for purely personal reasons," Team Sky said in a statement.
"Sean has been interviewed and there were no admissions or disclosures that would have required him to leave the team," Sky said.
In the wake of the Lance Armstrong doping scandal, Team Sky asked every member of the team to sign up to a written policy saying they have no past or present involvement with doping.
The 52-year-old Yates, the 1992 British champion, joined Team Sky in 2009 and led Bradley Wiggins to the Tour de France title this year.
He had been one of Armstrong's sports directors at Discovery Channel in 2005.
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