In a statement on Twitter, Ineos Grenadiers said the two-time time trial world champion had "displayed mild, flu-like symptoms.
"Filippo will now rest and recover fully before resuming his remaining 2023 race programme."
Ganna's absence will be a blow to teammates Geraint Thomas and Tao Geoghegan Hart, both of whom are in the top 10 of the overall standings.
Stage eight of the Giro d'Italia is a 207-km ride from Terni to Fossombrone.