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Ferguson was angered by linesman Simon Beck's decision not to award a penalty to his side after Wayne Rooney was brought down in the area while United led 1-0.
Tottenham equalised last weekend's game in stoppage time, leaving Ferguson to describe Beck's display as "shocking" and adding that the official had a history of failing to give United decisions.
In a statement on Tuesday the FA said Ferguson's comments had questioned the integrity of Beck.
"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 said.
"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 Friday afternoon to respond to the charge.
Should he be found guilty he could receive a touchline ban of up to four matches.