During an episode of the show broadcast earlier this month, the presenter commented on reports that some cyclists were now wearing cameras on their helmets to film the behaviour of some drivers.
Clarkson went on to detail an incident where a French cyclist had damaged his car, claiming that they "deserve" what happens to them on the roads.
In response to the complaints, the BBC published a statement from executive producer of Top Gear Andy Wilman reading: "Jeremy was singling out what he sees as aggressive cyclists, like the one who scraped his car. I don't think anyone can deny that, as with motorists, there are cyclists out there whose road behaviour is hardly ideal.
"Jeremy made it clear that in his view cyclists are free to use the roads as long as they behave themselves. Whilst he'd clearly prefer them to defer to motorists, I think his comments stop a long way short of encouraging aggression."
He added: "Of course Jeremy's views were balanced out by those of Richard Hammond, who stood up for cyclists."
Top Gear recently attracted complaints after featuring jokes about Mexicans.