Police and the English Football Association are investigating an allegation that Clattenburg used "inappropriate language" towards John Obi Mikel in last weekend's Premier League clash against Manchester United United at Stamford Bridge.
It is understood that the official strenuously denies any wrongdoing.
Chelsea have submitted a dossier of evidence to the FA containing accounts from players, who allege Clattenburg used a term which has been interpreted as racist, but the Manchester United manager has now spoken out in defence of the official.
Ferguson said: "I don't believe Mark Clattenburg would make any comments like that. I refuse to believe it."
The Scot went on: "I think it is unthinkable in the modern climate.
"I just don't believe it - simple as that. There is no way a referee would stoop to that, I am convinced of that."
Ferguson has infamously had many run-ins with referees during his near 26-year reign at Old Trafford but he believes in the integrity of the officials.
He said: "I think in the modern game, the way we see the game today rather than how it was 25 years ago, it has completely changed.
"I played myself and I know the banter that went on between referees and players 25 years ago is different from today.
"I have never heard a player come to me in the last 15 years and say a referee has sworn at them during a game, ever. So, that is where I stand. I don't believe it."