Buck says Chelsea have a "duty of care" for Terry even if he has done something wrong - he was banned for four matches for racially abusing QPR's Anton Ferdinand - and that the club would have been "crucified" if they had not reported to the FA allegations that Clattenburg used inappropriate language interpreted as racist towards John Obi Mikel.
Buck told the Evening Standard: "Suppose we had tried to sweep this under the rug and said to the various players, 'Look, it's not a big deal and the press are going to be all over us, maybe you want to reconsider'. If that had leaked out, we would've really been crucified."
He added: "The press seem to juxtapose 'our support' of John Terry and what's going on here and looking at us as being a bit hypocritical. We have to divorce the John Terry situation from this. From our perspective, the latest situation was pretty straightforward. We have an obligation to report what may be misconduct. We did that, in good faith and not maliciously."
Buck insists that Terry does not run the club but admits there has been numerous incidents involving the skipper.
He said: "We have a duty of care to John Terry in loco parentis. Not that, if he did something wrong, we weren't going to say he didn't do anything wrong. But we have to support him as a person. That's different from saying that, no matter what Terry does, we approve.
"I can't argue with the fact that, over the last 10 years, there have been a lot of public incidents in which Terry and Chelsea were involved. But I don't accept that we have something in our hearts that says we're going to chase the referees. It's just not like that at all, honest.
"Chelsea are not run by John Terry. I don't know how I can prove it to you but it's not true. My club is run by Roman Abramovich."
Buck also insisted the complaint against Clattenburg was not sparked by anger over the referee's decision during the 3-2 defeat by Manchester United. The official strenuously denies the allegations.
He said: "The reaction has been very unfair. We weren't interested in any confrontation with the referee or anybody else, had no thoughts of revenge on the referee. He made two obvious mistakes [sending Fernando Torres off and allowing Javier Hernandez's offside winner] which changed the tide."