Cavendish was taking part in the 11th stage, a 33km individual time trial from Avranches to Mont St Michel, when the incident happened.
Tour organisers have confirmed that a liquid was thrown at Cavendish, but there is as yet no official confirmation that it was definitely urine. Cavendish apparently believed it was water at first until the smell and taste told him otherwise.
Omega Pharma-Quick Step team manager Patrick Lefevere said: "I regret this, I always felt that cycling fans were gentlemen, enthusiastic people.
"Mark is sad, he's not upset, just sad. I cannot blame anyone, there are 100,000 or 200,000 people on the road, and one person decided to do this."
Jerome Pineau, a team-mate of Cavendish who hails from Northern France, revealed on Twitter that Cavendish had told him what happened during the 42-minute ride.
"Yesterday I was so proud of all the local support and encouragement along the route, but today I was ashamed when my friend Mark Cavendish told me that the fans were whistling at him and even threw urine at him during the ride. It's scandalous!"
The fact that the Manxman was targeted for abuse on Wednesday appears to be linked to the controversial end to Tuesday's stage, which saw Cavendish collide with opponent Tom Veelers during the final sprint for the line.
Veelers was outraged by what he believed was an elbow thrown his way, but Cavendish was not penalised over the incident and repeated viewings suggest that disqualification would have been very harsh, as Eurosport blogger Blazin' Saddles has explained.