Ferguson branded Beck's performance "shocking" after he failed to flag for what the Scot thought was a "clear penalty" for the visitors when Wayne Rooney went down in the box after a challenge by Steven Caulker in United's 1-1 draw at Tottenham.
The United boss said his club had "history" with Beck following his failure to rule out an offside Didier Drogba goal in 2010 and also claimed that: "There was no way we were going to get a decision from (Beck)."
He was charged by the FA on January 29, but has responded and requested a hearing.
"It is alleged the Manchester United manager breached FA Rule E3 in that he implied that the match official was motivated by bias," the FA confirmed in a statement.
"Ferguson has requested a paper hearing, the date of which will be set in due course."
Ferguson did not discuss the issue during his press briefing on Friday, 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."