The Hull City manager believes the governing body have badly misjudged the incident involving his forward and Joe Hart, who avoided action despite his part in the spat
The Hull striker was charged with spitting at the Manchester City goalkeeper but Bruce has questioned how a decision was made and defended Boyd's part in the incident.
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"We don't know who's on it, who makes the decision, who's accountable for it. We just get the decision that the FA are charging by three refs who looked at it and they're not going to go against the others."
"We're all totally disappointed for George. I've had the privilige to manage him for the best part of a year and know for a fact he would never, ever spit at anyone deliberately and he is genuinely horrified with the charge.
"I'm 100 per cent behind him. The problem is we can't go down and see anybody represented on this commission. We don't know who sat on it, who took it. We're just totally disappointed that the whole system, for me, needs to be looked at."
Bruce also questioned why Hart himself was not punished for his involvement, with the England goalkeeper seen exchanging fierce words with the Hull striker.
"[I've got] Nothing against Joe Hart but I don't know how he gets away unpunished if you're going to do George Boyd," Bruce added.
"As I said, for George himself he feels that strongly about it if there was legal action to take, he'd take it because he's accused of something which is not in his make-up. I've managed players capable of it but not George Boyd.
"Joe Hart has come out and said he didn't deliberately spit on him but as soon as he was charges. We all understand that they're not going to change it and I don't know why this so-called committee sits, we don't know who's on it. We're not represented on it and, for me, we don't get a fair hearing."
"You can see it on the television. You can see a bit of spit come out of his mouth as he's shouting at him. That's not deliberate. And I'll reiterate that George Boyd does not have this in his locker."
Hull host West Bromwich Albion on Saturday in a clash that could hold heavy significance for the bottom half of the table.