Club chairman Bruce Buck told the Evening Standard newspaper on Tuesday that the two controversies must not be linked and said that ultimately the club had no choice but to report the referee.
"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," said the American.
"We have to divorce the John Terry situation from this," he added. "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."
European champions Chelsea lodged a complaint with the Football Association last month over language allegedly directed at Nigerian John Obi Mikel by Clattenburg during a Premier League defeat to Manchester United.
Clattenburg, one of the country's top match officials who sent off two Chelsea players at Stamford Bridge, has not refereed for the last two weeks and will not be in action this weekend either.
The claims against the referee have been questioned publicly by several leading football figures, including Manchester United manager Sir Alex Ferguson.
"The reaction has been very unfair," said Buck. "We weren't interested in any confrontation with the referee or anybody else, had no thoughts of revenge on the referee."
He said the decision to take action had come after a "great deal of anguish and after talking long and hard that evening about what we should do."
"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," added the chairman.
Buck said he had spoken to the players concerned, for whom English was not a first language, three separate times after the match and asked them if they might have confused 'monkey' with 'Mikel'.
Asked whether the referee might have used the phrase 'I don't give a monkey's...", Buck confessed he was not familiar with the expression.
Buck said the formal complaint, after witness statements had been taken by external lawyers, was made by the Chelsea management without pressure from the players.
He stressed that Chelsea were not run by Terry, who remains club captain despite serving a four match ban and being fined 220,000 pounds by an independent FA panel for racially abusing Queens Park Rangers defender Anton Ferdinand.
