Patrick Lefevere of Omega Pharma-Quick Step said the incident may have been linked to anger among some fans who claimed — unfairly in his view — that Cavendish intentionally bumped into Dutch rider Tom Veelers and caused him to crash in the final sprint a day earlier.
"(Cavendish) explained to the other guys in the bus that the public was not very fair with him, and then somebody put some urine on him," Lefevere told The Associated Press after Stage 11.
"We are always happy in cycling that there is no hooliganism, but of course, when there are 100,000 or 200,000 people on the road ... somebody had bad behaviour," he added.
After the stage, it did not appear that Cavendish had spoken publicly about the incident.
The liquid thrown at Cavendish smelled like urine and was "all over him," team spokesman Alessandro Tegner said. The team didn't know exactly where it happened on the 33-kilometre (20-mile) course to Mont-Saint-Michel on the Brittany coast.
Cavendish's teammate, Jerome Pineau, reacted angrily to the news.
"I'm ashamed when my friend Mark Cavendish tells me that he was jeered and even sprayed with urine," Pineau said on his Twitter feed. "It's scandalous."
Race leader Chris Froome of Britain said it was disappointing to hear about the incident.
"Mark, he's one of the big characters in the sport, and some people love him and some people hate him. But to do something disrespectful like that, that's really sad," he said. "One individual doing that, it just leaves a bit of a bad taste in your mouth — a bad taste in Mark's mouth!"
At least one cycling aficionado suggested it was all part of the sport.
Lance Armstrong tweeted: "why all the sudden shock and outrage. this has been happening for 100 years in some form or another."
Cavendish, fourth all-time with 24 Tour stage wins, was adamant that his bump with Veelers wasn't deliberate. Veelers said Cavendish knocked him over, though the Dutchman's Argos Shimano teammate Marcel Kittel of Germany, who won Tuesday's stage, gave the Briton the benefit of the doubt.
The race stewards did not sanction Cavendish over the incident, a sign they don't believe he was to blame.
The millions of fans who throng the roadsides often use the passage of Tour riders as an opportunity to picnic, wave flags, and deliver political or other messages aimed at TV cameras on helicopters overhead. The free, non-ticketed event offers closer access for fans to athletes than at many other sports competitions.
A spectator once punched five-time champion Eddy Merckx in the kidneys.
Lefevere noted that on the legendary Alpe d'Huez — which the pack will scale not once but twice in Stage 18 next week — has often been known for rowdy fans who douse passing Tour vehicles with beer: "They do it on our cars as well, so we ride with closed windows ... it should not happen."
AP Sports Writer John Leicester contributed.