Speaking on ITV1's The Jonathan Ross Show, the Top Gear presenter was discussing the row involving Argentina.
The show's stars and crew had to abandon filming earlier this year in the country after angry protests to a number plate which appeared to refer to the Falklands War.
Clarkson repeated assurances that the H982 FKL plate was purely coincidental.
Some said that it was an intentional reference to the 1982 Falklands War, between the UK and Argentina.
Clarkson told Jonathan Ross: "If we had done it on purpose - and we didn't - it didn't warrant the reaction we got. The reaction was horrible.
"I've never been chased out of an entire country.
"Some of our guys were injured. Rocks were thrown at every single car. The only good thing was our first assistant director saying that they (the Argentines) throw like girls."
"We hadn't gone down there to upset anybody. It was genuinely scary.
"Sometimes we ask for it but it all went hideously wrong."
The Top Gear special saw Clarkson and co-stars Richard Hammond and James May drive the famous Patagonian highway - Route 40 - to the southern city of Ushuaia.
The BBC has refused to apologise to Argentina for the episode.
Earlier this year, Argentine ambassador Alicia Castro met BBC Director of Television Danny Cohen to demand a formal apology.
In a letter to her, Mr Cohen said: "I am very aware that some have questioned whether the number-plates were in some way a prank.
"I would like to reassure you again that nothing we have seen or read since the team returned supports the view that this was a deliberate act."
The BBC still intends to broadcast the programme this Christmas.
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Never one to shy away from controversy, Jeremy Clarkson's been describing what he's called his "difficult year."