The Manchester United manager criticised assistant referee Simon Beck following his side's draw at Tottenham 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."
Speaking after the Tottenham game, Ferguson expressed his anger at United not being given a penalty for a foul on Wayne Rooney.
"It was a clear decision. And he [Beck] was 10, maybe 12 yards away from the incident and he doesn't give it. And yet he gave everything else."
Ferguson claimed United had "history" with Beck following the official's failure to rule out a Didier Drogba goal for offside at Old Trafford in 2010, in a match that proved pivotal in that season's title race.
"There was no way we were going to get a decision from [Beck]," Ferguson said.
Clearly the United manager's argument is that he should be allowed to criticise Beck, which is why he is taking the matter further even though the likely punishment if the case is proved is only likely to be a fine.
Ferguson did not discuss the issue today, although last week he said he suspected the matter has become personal.
"That is what I have put in my letter exactly. But you never know the FA," he said.
"We are high profile and the profile of me is such that the FA naturally panic as soon as the press criticise them.
"I think that is what you will find. That is why they have sent me a letter.
"Whether I think it is unfair or not doesn't matter to them really at this point.
"I just think it is more about me than what I have said."