Coates was quoted by The Sentinel earlier this month as saying "there does seem to be a bias towards other teams" regarding referees' decisions in Stoke matches.
The FA released a statement on Thursday which said: "Peter Coates has been charged by The FA for misconduct in relation to media comments.
"It is alleged the Stoke City chairman made comments which constitute improper conduct in that they allege and/or imply bias on the part of referees and/or bring the game into disrepute.
"He has until 6pm on 24 November 2014 to respond to the charge."
The chairman's comments had come just a few days after Stoke boss Mark Hughes' angry complaint that a challenge by Alex Song on Potters forward Mame Biram Diouf had not resulted in play being stopped during West Ham's 2-2 Barclays Premier League draw at the Britannia Stadium
The unpunished, rash-looking tackle from on-loan Barcelona midfielder Song came in the build up to the Hammers' first goal.
Stoke's previous two home games had seen their striker Peter Crouch being sent off and captain Ryan Shawcross have a penalty awarded against him for grappling at a corner.
Coates was quoted as saying on November 4: "We feel we don't always get fair treatment and that is all we are asking for.
"There does seem to be a bias towards other teams
You always feel that because we have a good crowd that gets behind the team, referees seem to think 'I will show them who's in charge here.' Perhaps it's a macho thing.
"You do get a bit fed up getting fouls against us and decisions having an effect on games, such as a two-footed challenge that doesn't even get a booking or a foul
I do feel that we get treated more harshly than the opposition."
Higginbotham, who was with the Staffordshire outfit for the 2006-07 season and then from 2008 to 2013, says he has "all the sympathy in the world" for Coates.
He added in The Sentinel: "You can see why owners, chairmen, managers and players are getting so frustrated, because referees are not answerable for their decisions.
"Referees should be made to come out and explain their decisions after a game, then people like Peter Coates wouldn't have to come out and say things like that."
Stoke did not wish to comment on the matter when contacted by Press Association Sport.
Source : PA
Source: PA