For years the identity of the driver has been a closely guarded secret but he was apparently unmasked last week as professional stuntman and Le Mans racer Ben Collins.
Writing in The Sun on Saturday Clarkson criticised the fact that The Stig's name had apparently been revealed and said it had "spoiled everyone's fun".
He added that speculation had become so intense that "even Top Gear researchers are being followed by the paparazzi."
He wrote: "I've decided it's time to come clean. For still photographs, there are indeed many Stigs. But there is only one who is ever allowed to drive round the track.
"And - here goes - it's the BBC royal reporter Nicholas Witchell. I know. I know. It's a big surprise but there you are. And now you know, I'm afraid he will have to be dropped from a Hercules transport plane and killed."
Clarkson, 48, dismissed the speculation over The Stig's identity by further mocking the rumour-mongers.
He wrote: "They're wrong. There is no single Stig. There are four. The main one is Damon Hill. It's Tiff Needell.
"No it's not. I've got a mate who knows for sure it's Michael Schumacher
