Manchester United chief executive David Gill claims the Football Association singled out the club for "harsh" punishments which would not have been imposed on their Barclays Premier League rivals.
United found themselves involved in two high-profile disciplinary hearings last season. Striker Wayne Rooney was banned for two matches for swearing into a television camera during the team's victory at West Ham in April while manager Sir Alex Ferguson was handed a five-game touchline ban for comments made about referee Martin Atkinson.
"I do genuinely believe there have been some poor-ish decisions that, in my opinion, wouldn't necessarily have hit other clubs," United's chief executive said in Champ19ns, a book about the club's record title-winning season.
"That's not to say I'm condoning Wayne's comments, because I don't think they were correct, or what Sir Alex said, because it wasn't helpful. But at the same time, the actual punishments were harsh.
"We're possibly being caught up in being one of the biggest clubs and the (FA's) Respect agenda being there. What better way to demonstrate the authorities are being tough than by hitting one of the biggest clubs the hardest?"
Gill believes the FA's treatment of Rooney for his swearing episode has set a precedent but questioned whether the governing body would apply the same sanction to other players in the future.
"The club doesn't condone it but Wayne recognised it was wrong and apologised almost immediately,' he added.
"We have various issues with the ban - one being consistency. What's going to happen now? Is the referee under pressure to send everyone off?
"It's a dangerous course the FA has gone down, because consistent application is what's required and I'm not sure that will necessarily happen.
"There are certain things you should wait until the start of the season to change."