Mourinho claimed there is a "clear campaign by "people, pundits, commentators and coaches from other teams" against Chelsea and labelled the booking of Cesc Fabregas for diving in a 1-1 draw at Southampton on December 28 as a "scandal".
"It is alleged his remarks constitute improper conduct in that they allege and/or imply bias on the part of a referee or referees and/or bring the game into disrepute," a statement issued by the FA read.
Chelsea had been at the centre of a debate over diving when Mourinho made the comments.
Diego Costa and Willian were booked for simulation against Hull on December 13, prompting Steve Bruce to describe a Gary Cahill dive as being "like something out of Swan Lake".
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The west London club faced renewed scrutiny on Boxing Day when Branislav Ivanovic appeared to take a tumble against West Ham, the type of incident Mourinho believes is being unjustly scrutinised to Chelsea's detriment.
"People, pundits, commentators, coaches from other teams - they react with Chelsea in a way they don't react to other teams.
"They put lots of pressure on the referee and the referee makes a mistake like this."
The FA also reviewed comments made by Mourinho on December 19, three days before the victory in Stoke, in which he spoke about the need for a "good, experienced referee". Neil Swarbrick oversaw the match
"Having sought Mourinho's observations on this matter, the FA has decided not to bring a disciplinary charge and has instead issued a formal warning," the FA statement read.