Chelsea made a formal complaint over Clattenburg's behaviour during last Sunday's 3-2 Premier League defeat to Manchester United, but Ferguson said he "refuses to believe" the referee is guilty.
"In the modern climate I just refuse to believe it," he said in his Friday morning press conference. "I don't believe Mark would make any comments like that. It's unthinkable."
Ferguson added: "I've never had a player come to me in the last 15 years and say a referee has sworn at him."
Chelsea's complaint to the FA concerns a confrontation between Clattenburg and Mikel - reports claim Chelsea believe the official used the word "monkey".
A club statement said: "This is a result of a thorough investigation carried out by the club, and led by outside legal counsel, of all information available to us including interviews with a number of players and staff."
The Metropolitan Police is also investigating the incident.
However, Chelsea have come under fire from managers, with Ferguson joining Arsene Wenger and Sam Allardyce in voicing their misgivings over their actions.
Wenger said on Thursday: "My opinion is that I prefer, when I didn’t behave well, that I have an explanation with the referee at the end of the game, or on another day, than going public with little proof.
"I'm not a great believer in making these stories public. One of the great things in sports is tolerance, forgiveness and explanation internally and I think it should stay like that.
"It can happen that a referee doesn’t behave well. I do not say they are angels, but it is always better to sort it out in the room."
It is also believed Clattenburg's fellow officials, who had an audio link to the referee during the match, will defend the 37-year-old.
Meanwhile, police are still looking for a man who appeared to make a monkey gesture towards Danny Welbeck in Chelsea's Capital One Cup match against United on Wednesday night.
Chelsea travel to Swansea City on Saturday, when John Terry completes his four-match ban after the FA found him guilty of racially abusing QPR's Anton Ferdinand last season.
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