The Manchester United manager criticised assistant referee Simon Beck following his side's draw at Tottenham in the Premier League a fortnight ago.
The Football Association will decide a date for the hearing in due course.
The FA said in a statement: "Sir Alex Ferguson has denied an FA charge of misconduct in relation to post-match media comments made following Manchester United's game at Tottenham Hotspur on Sunday 20 January 2013.
"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 requested a paper hearing, the date of which will be set in due course."