The popular BBC show was in Argentina over the past few weeks to shoot an end-of-season special across parts of South America.
As is common for these scripted races, the three hosts each chose a clapped-out, second-hand car for their journey, with a Porsche 928, a Lotus Esprit and a Ford Mustang being the presenters' final selections.
Clarkson's Porsche carried the numberplate "H982 FKL". This, according to Patagonian newspaper Diario Jornada, was interpreted by locals to be a reference to the two month war fought between Britain and Argentina over the Falkland Islands in 1982.
As can be seen in the video, above an angry mob pelted the show's cars in the presence of a police escort.
According to producer Andy Wilman, "Top Gear production purchased three cars [in the UK] for a forthcoming programme; to suggest that this car was either chosen for its number plate, or that an alternative number plate was substituted for the original is completely untrue."
Clarkson has taken to Twitter to defend himself and the TV show. Yesterday he tweeted, "All TG crew now safely out of Argentina. I just got back to UK."
He continued, "The number plate WAS a coincidence. When it was pointed out to us, we changed it. As pics in this morning's Mail show." Clarkson later posted a photo (above) on the social media site of the Porsche 928 without its British number plates.
"This was not a jolly jape that went awry. For once, we did nothing wrong ... They threw us out for the political capital. Thousands chased crew to border. Someone could have been killed ... And these war veterans we upset. Mostly they were in their 20s. Do the maths," he concluded.
A BBC spokesman said, "We're pleased the team is safe and would like to thank all of those who have helped. As the executive producer has made clear, the number plate issue is a very unfortunate coincidence."
The Top Gear TV show is no stranger to controversy, with previous incidents involving Clarkson's alleged use of the N-word and offensive remarks about Mexicans.