Following an internal investigation, Chelsea decided to rescind the complaint of referee Mark Clattenburg using "inappropriate language" towards Juan Mata, but pressed ahead with a formal complaint over the treatment of John Obi Mikel.
Clattenburg has reportedly been accused of using a word of a racial nature towards Mikel during the controversial English Premier League game against Manchester United at Stamford Bridge Sunday.
"Chelsea Football Club today lodged a formal complaint with The Football Association regarding inappropriate language directed at John Mikel Obi by referee Mark Clattenburg." The club said in a statement.
"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.
"Board members began establishing the details of the allegations, speaking to all relevant players and staff. After those initial interviews, it was clear that the matter had to be reported.
"The correct protocol for doing so was to report the incidents to the match delegate, and the club took immediate steps to inform him as soon as he was available. It was not a decision the club took lightly.
"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.
"There was not sufficient evidence to support a second claim to the FA with regard to the alleged verbal abuse of another first-team player."
The FA are already carrying their own investigation into the allegations, with the Metropolitan Police also making an inquiry. "We will cooperate fully with the FA and the police as they each investigate the matter," the statement added. "As events on Sunday are now subject to those investigations, we are unable to comment further until those processes are complete."
Clattenburg has reportedly denied the allegations, and has vowed to cooperate fully with the investigation. The 37-year-old and the assistant referees, were reportedly stunned by the allegations, with the linesmen, who were miked up during the game, saying, according to sources, they had not heard anything inappropriate.