Graham Bean, part of Sir Alex Ferguson's defence team, has made the astonishing accusation in an interview with ESPNsoccernet, suggesting the FA acts "like a Communist State".
Bean, whose company Football Factors has defended Ferguson on numerous previous disciplinary issues, is livid at the way the FA treated the Manchester United boss.
Ferguson has opted not to appeal and has notified the FA of his decision with his five game ban taking immediate effect. But, while the Manchester United manager is keeping his own counsel on his true feelings, Bean slammed the decision.
"What everyone has missed because they have focused on this big ban on Sir Alex, is that Martin Atkinson made one of the biggest blunders of the season in not dealing with David Luiz and he has got off with it, nothing has happened to him,'' he told ESPNsoccernet.
"That cannot be right that the ref is protected in that way, and then the FA hammer Sir Alex. I have seen confidential reports where Atkinson is criticised by the assessors at the game in the way he dealt with David Luiz, and that he didn't deal with the incident the way he should have done.
"The FA has become like a Communist State in the way that you cannot speak out against authority. It is becoming clear that if you are in football you give up your right to freedom of expression.''
The FA was unhappy with comments Ferguson made following a controversial 2-1 defeat at Chelsea, when the United boss said he had "feared the worst" when Atkinson was appointed match official for the Premier League clash on March 1, adding: "You want a fair referee, or a strong referee anyway - and we didn't get that."
Bean, the first FA compliance officer, claimed that the 'fair' comment played no part in the decision to ban him from the touchline.
"Mangers and players cannot say anything against authority without fear of such action,'' he added. ''Yet Sir Alex was making the point, he was alluding to the fact that the game needed a strong referee. "It had nothing to do with Sir Alex suggesting he wanted a fair referee, he didn't say that. He qualified his words but the FA did not accept that. As for the five game ban, it is three games, plus two from a previous case from 2009, which had a two game suspended and which would have expired at the end of this season.
"It was also at the discretion of the current panel to invoke that two game ban, and they chose to do that. The only saving grace is that it is simply a touchline ban and doesn't go as far as the UEFA ban.
"It means that Sir Alex is only barred from sitting on the bench for the next five games starting against Bolton on Saturday. He has chosen not to appeal, because he just wants to get on with it, but you can take it from me he is not happy about it.''
Ferguson will now return to the dugout for the game with Arsenal at the Emirates that could have a major impact on the destination of the Premier League title.