Sir Alex Ferguson hit out at the Football Association after Manchester United chose to accept a charge of violent conduct against Wayne Rooney.
Rooney was charged after clashing with Bolton's Tal Ben Haim on 26 December.
The England striker will be suspended for three games, starting with the trip to Middlesbrough on 1 January.
Ferguson described the FA's new disciplinary system as "completely flawed" and "immoral" after deciding against lodging an appeal.
The charge arose after Rooney shoved Haim in the face, and the Israeli appeared to over-react by falling to the ground.
Bolton have said they will contest Ben Haim's charge of improper conduct, although manager Sam Allardyce has conceded that his player "went down rather too easily".
Ben Haim himself said: "I want to say clearly that when Rooney hit my face I genuinely fell down out of instinct."
GAMES ROONEY WILL MISS
Middlesbrough (away, 1 Jan)
Tottenham (home, 4 Jan)
Exeter (home, 8 Jan)
Rooney will be suspended for the trip to Middlesbrough and the home games against Tottenham and Exeter in the Premiership and FA Cup respectively.
He will then be available for the Carling Cup semi-final first-leg at Chelsea on 12 January, as well as the crucial league visit to arch-rivals Liverpool three days later.
Ferguson is angry that under the FA's new protocol a club cannot be represented at a disciplinary hearing should a player deny a charge.
"The system is completely flawed," said Ferguson. "The problem for us now is we can't really appeal
because we are not allowed to be represented. It is a closed session.
"So therefore they are telling you that you need not bother appealing because we're not going to win anyway.
"As we are approaching 2005, that seems to be unfair and immoral."
And Ferguson questioned the decision to charge Rooney with violent conduct.
"The violent conduct charge bemuses me because every man and his dog would agree it was not violent conduct," said Ferguson.
"If it is violent conduct why are they charging Ben Haim? I can't understand it. He (Ben Haim) is being charged so they therefore believe he is guilty of diving and bringing the game into disrepute."