The United boss blasted assistant referee Simon Beck for a missed penalty call on Wayne Rooney after his side drew 1-1 at Tottenham earlier this month and was asked to explain his comments to the FA.
Despite that since occurring, the FA have decided that Ferguson has to be accountable for his words.
"The FA has today (Tuesday 29 January) charged Sir Alex Ferguson in relation to post-match media comments made following Manchester United's game at Tottenham Hotspur on Sunday 20 January 2013," said an FA statement.
"It is alleged the Manchester United manager breached FA Rule E3 in that he implied that the match official was motivated by bias.
"Ferguson has until 4pm on Friday 1 February 2013 to respond to the charge."