Ferguson will have to answer to the FA for remarks criticising assistant referee Simon Beck.
United had drawn with Tottenham 1-1 at White Hart Lane and after the game Fergie said: "I think we should have had a throw-in down our side of the pitch but that linesman never gave us a thing all day.
"For me, it was a poor performance by him. He never saw the penalty kick for Wayne Rooney and some other decisions too.
"We remember him well from his time at the Chelsea game [in 2010] when Didier Drogba was three yards offside and he gave onside. I think he had a shocking game today and I'm disappointed in his performance, I really am.
"I think he has had a bad game and we never got anything from that side of the pitch. We got a bad break."
On Tuesday, an FA statement read: "The FA has today 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.
"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."