Clarkson and Richard Hammond decided to dress in niqabs, a form of the burka where everything but the eyes is covered, in order to disguise themselves on the road. They also got James May in on the act when they greeted him from hospital after he fell and hit his head on rocks in the Syrian desert.
But their joke backfired after Muslims slammed them for mocking their religion. "The burka is a symbol of our religion and people should not make jokes about it in any way," the Daily Mail quoted Islamic extremist Anjem Choudary, as saying.
"It would have been equally bad even if they'd not been in a country mainly populated by Muslims," Choudary added.
On the Boxing Day episode of the show, the trio was driving across the Middle East to follow the path of the Three Wise Men.
In the episode, which was watched by six million people, they drove specially customised sports cars to Bethlehem via Turkey, Syria and Jordan.
While in Syria, their cars got stuck in the sand and as Clarkson was trying to tow Hammond out, May, who was holding the rope between the two cars, was knocked to the ground when it went taut, cutting open his head in the process.
With blood pouring from his head, he was taken to hospital and Clarkson and Hammond carried on when they had an idea to disguise themselves as women in burkas so not to be seen diverting from the sands of the desert to a road.
They then greet May from hospital dressed head to toe in niqabs before hitting the road again. But their choice of attire caused a storm online on Twitter and other discussion sites.
This is not the first time Clarkson has caused a storm over a burka. In July this year he told Top Gear viewers that he had seen a Muslim woman wearing saucy underwear beneath her gown.