It is believed the liquid was thrown at the 28-year-old Omega Pharma-QuickStep rider as he took part in a time trial from Avranches to Mont Saint Michel.
Cavendish was involved in another controversial incident on Tuesday as he crashed with Dutch rider Tom Veelers.
Following accusations that the liquid thrown was urine, Cavendish's teammate, Jerome Pineau, said on Twitter: "Yesterday I was so proud about the support but today I am ashamed. Shame on you.
"Ashamed when my friend Mark Cavendish tells me he has been whistled and even sprayed with urine on the course. It's scandalous."
Cavendish featured among the early runners in the trial and clocked a time of 42 minutes.