Ferguson was charged with improper conduct by the Football Association for his outspoken post-match attack on Atkinson following United's 2-1 defeat at Stamford Bridge on Tuesday.
The Scot, who Press Association Sport understands has decided to appeal the charge, appeared to question the official's integrity when he said "in matches like this, you want a fair referee" during an interview with his club's in-house television station, MUTV.
Chelsea boss Ancelotti has described Ferguson's reaction as "normal", saying: "After the game, you have emotion about the game so, sometimes, you speak about decisions. This is normal, I think."
He added: "He had an argument against the referee. But I don't want to comment on this. I have a fantastic relationship with Sir Alex.
"We spoke after the game and he was disappointed at the referee's decision, but this is football. Sometimes one coach is happy and the other is unhappy after a match with a referee's decision."