The 29-year-old Italian rider has been plagued by an inflammation of the outer ear and ear canal in recent days according to the team's doctor.
"Cunego began to feel bad sensations during the afternoon and then he began to have temperature," Dr Ronchi explained. "It was due to the otitis externa [ear infection] and to a beginning of pharyngitis, that won't allow him to be tomorrow at the departure."
It was originally thought that he would race, despite his illness, however with the situation not improving the decision was taken to withdraw him.
Cunego will not be replaced by the team and will take on the five stage race with seven riders.