Sir Alex Ferguson and assistant Carlos Queiroz have been charged with improper conduct following their criticisms of refereeing standards, following Manchester United's FA Cup exit last month.
Ferguson and later Queiroz slammed the performance of match referee Martin Atkinson following United's 1-0 sixth round defeat to Portsmouth at Old Trafford on March 8.
United were denied a first-half penalty when Cristiano Ronaldo went down in the box under a challenge from Sylvain Distin and they also saw goalkeeper Tomasz Kuszczak sent off in the second half.
After the match the veteran Scot also rounded on Professional Game Match Officials Board chief Keith Hackett and accused the referees' boss of favouritism in his choice of officials.
The Football Association initially wrote to both Ferguson and Queiroz seeking an explanation of their comments before issuing charges.
"Manchester United manager Alex Ferguson and assistant manager Carlos Queiroz have both been charged with improper conduct," read an FA statement.
"Ferguson's charge concerns comments about referee Martin Atkinson and PGMO general manager Keith Hackett.
"Queiroz's charge relates to comments about referee Martin Atkinson. Both parties have until April 17 to respond to the charge."
Immediately after the defeat, Ferguson had said: "It's absolutely ridiculous. I cannot explain it. Managers get sacked because of things like that and he's going to referee a game next week.
"Martin Atkinson will referee next week, no problem, but his performance should not be accepted in our game."
Queiroz himself added: "I feel sorry that the game has moved to the situation where referees deserve red cards.
"The referee is a disgrace. We did our job, Portsmouth did their job, but the referee didn't.
"Sadly, we still have referees who don't understand what is the right thing in the game and who they should be protecting."