Cavendish, who first thought it was water, made the stomach-turning discovery by tasting the liquid.
The 28-year-old declined to comment on the incident but that didn't stop his team manager, Patrick Lefevere, from expressing his disappointment.
"Probably some spectators were not very pleased with what happened yesterday and they yelled to him and then one other idiot threw urine at him," Lefevere said in reference to Cavendish’s crash with Tom Veelers near the end of Tuesday’s 10th stage. "I regret this. I always felt that cycling fans were gentlemen, enthusiastic people."
"Yes, that's true I think. I was behind him. I didn't see it, but I think it's true," Omega Pharma-Quick Step team press officer Alessandro Tegner said.
Tegner said the liquid smelled like urine and it was "all over him," and said Cavendish talked about the incident after completing the time trial.
"He said: 'I really don't know what's going on,'" Tegner said.
Tegner said the team does not know exactly where it happened on the 33-kilometer (20-mile) time-trial course to Mont-Saint-Michel on the Brittany coast.
Disgraced cyclist Lance Armstrong didn’t see what all the fuss was about in expressing his opinion on Twitter. "why all the sudden shock and outrage. this has been happening for 100 years in some form or another," he tweeted.
@dwuori why all the sudden shock and outrage. this has been happening for 100 years in some form or another. piss, spit, fists, etc.
— Lance Armstrong (@lancearmstrong) July 10, 2013
"It ruins the whole atmosphere for the spectators coming to the sport. One individual doing that just leaves a bit of a bad taste in the mouth,” Tour leader Chris Froome said. “And a bad taste in Mark's mouth.”
That's one way to get a yellow jersey.