The Stamford Bridge side has followed "correct protocol" and made the matter official after the club believes the referee used inappropriate language towards its midfielder
The club has also not decided to follow up a second count of alleged abuse from the referee to another Chelsea player due to "insufficient evidence."
The incident was said to have taken place during the Stamford Bridge side's 3-2 defeat at home to Manchester United on Sunday afternoon.
The statement reads: "Chelsea Football Club today lodged a formal complaint with The Football Association regarding inappropriate language directed at John Mikel Obi by referee Mark Clattenburg.
"This is a result of a thorough investigation carried out by the club, and led by outside legal counsel, of all information available to us including interviews with a number of players and staff.
"Following Sunday's Premier League game against Manchester United, club board members were quickly made aware, upon entering the home dressing room after the final whistle, that there were allegations of inappropriate language directed at Chelsea FC players by Mr Clattenburg during the game."
The club revealed once board members learned of the details surrounding the allegations, the only course of action was to report the incident to the match delegate, which "was not a decision the club took lightly."
The statement continued: "Since reporting the matter to the delegate, the club and outside legal counsel have conducted further investigations. Having completed that process we have now followed the correct protocol and lodged a formal complaint with The FA regarding John Mikel Obi.
"We will cooperate fully with The FA and the Police as they each investigate the matter. As events on Sunday are now subject to those investigations we are unable to comment further until those processes are complete."