"The charge relates to comments made about match official Martin Atkinson in post-match interviews following Manchester United's fixture with Chelsea at Stamford Bridge on Tuesday," the FA said on its website.
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Ferguson criticised Atkinson after Chelsea came from behind to win the game with a Frank Lampard penalty awarded after Chris Smalling was ruled to have tripped Yuri Zhirkov.
Fergsuon was also angry that Chelsea's Brazilian defender David Luiz, who volleyed the equaliser, escaped a red card after a second-half challenge on Wayne Rooney.
"It was a major game for both clubs and you want a fair referee," Ferguson said in an interview after the game. "You want a strong referee anyway and we didn't get that.
"I don't know why he's got the game. I must tell you, I must say that when I saw who was refereeing, I feared the worst."
The defeat, United's second in the Premier League this season, blew the title race wide open with Ferguson's side still four points above Arsenal who now have a game in hand.
Ferguson has until March 8 to respond to the charge.
