Ferguson has until 4pm on Tuesday, March 8 to respond to the charge, which relates to comments made about referee Martin Atkinson immediately after Manchester United's Premier League defeat at Chelsea.
The United boss was fuming at Atkinson over his failure to dismiss Chelsea goalscorer David Luiz for clear fouls on Javier Hernandez and Wayne Rooney after the Brazilian had already been booked.
Furious: Sir Alex makes his point during Manchester United's defeat to Chelsea at Stamford Bridge on Tuesday
To compound that frustration Atkinson then awarded Chelsea what he considered a 'soft' penalty when Yuri Zhirkov fell under Chris Smalling's challenge.
Although Ferguson's comments to host broadcaster Sky Sports are not thought to have overstepped the mark, those to United's in-house TV station MUTV have caused concern.
Raging: Ferguson was fuming that Luiz didn't receive a second yellow for this off-the-ball trip on Rooney
'You want a fair referee, or a strong referee anyway - and we didn't get that,' said Ferguson in the aftermath of the 2-1 defeat.
'I must say, when I saw who the referee was I feared it. I feared the worst.'
The Football Association asked MUTV for footage of the interview to check the context in which Ferguson delivered the words.
Off: United defender Vidic is shown a red card by referee Atkinson after a second booking at Stamford Bridge
And, even though he immediately soften his stance, altering the word 'fair' to 'strong', disciplinary chiefs feel there is sufficient malice to warrant charging him in a week when Wayne Rooney escaped further punishment for elbowing James McCarthy at Wigan last week.
Even Ferguson accepted his star striker had been 'fortunate'.
The Scot, who has decided not to hold a press conference ahead of Sunday's FA Cup tie with Liverpool, has not been so lucky and unless he can persuade the FA of his innocence, is facing a lengthy period away from the dug-out.
'Soft': Fergie wasn't happy with the penalty awarded to Yuri Zhirkov (centre, on the ground)
Ferguson already has two matches of a four-game ban still hanging over him following his ill-advised comments about Alan Wiley last season, when he implied the official was not fit enough for his job.
Those games will be triggered if guilt is established, which would condemn him to the stands for United's FA Cup sixth-round tie with Arsenal at Old Trafford on March 12, plus the Premier League encounter with Bolton seven days' later.
Punishment for his latest indiscretion would be added.
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Explore more:People: Alex Ferguson, James McCarthy, Wayne Rooney, Yuri Zhirkov, Martin Atkinson Places: Liverpool Organisations: Football Association