The referee stands accused of directing racist comments at Chelsea midfielder John Obi Mikel during United's 3-2 win at Stamford Bridge last Sunday.
The matter is being investigated by the Football Association and the Metropolitan Police while Chelsea are conducting their own internal inquiry.
But Ferguson said: "I don't believe Mark Clattenburg would make any comments like that. I refuse to believe it.
"I think it's unthinkable in the modern climate. I just don't believe it. It's as simple as that. There's no way a referee would do that or stoop to that, I'm convinced about that.
"I think that the modern game that we see today, as opposed to 25 years ago, has completely changed.
"I played myself and I know that the banter that went on between referees and players 25 years ago is completely different from today.
"I've never had a player ever come to me in the last 15 years to say that a referee ever swore in a game, ever."