The Scot was furious United were not awarded a penalty at White Hart Lane when Wayne Rooney appeared to be tripped by Steven Caulker in the home side's box.
He said afterwards: "There was no way the linesman was going to give that - he gave them everything.
"It was a clear decision. And he was 10, maybe 12 yards away from the incident and he doesn't give it. And yet he gave everything else."
But Ferguson has chosen to fight the charge, as confirmed in a statement on the FA website, which read: "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."
The Premier League leaders were ahead for much of the game through a Robin van Persie header - only for Clint Dempsey to pop up in injury time and sweep home Aaron Lennon's cross, ensuring a stalemate.