Bouhanni was widely expected to win the French road championships at the weekend but crashed as the race reached its conclusion, injuring his ribs in the accident.
Initially his participation in the Tour was not thought to be in doubt. But he later took to Twitter to say he was probably out of the race.
“Certainly out of the Tour. Rib cracked or broken…I’ll update soon. “No words to describe my sadness and disappointment," Bouhanni said.
Cofidis had built its Tour de France ambitions almost entirely around Bouhanni after he won two stages of the Vuelta a Espana and three at the Giro d’Italia last year.
He had been selected for the Tour along with Geoffrey Soupe, Florian Senechal, Christophe Laporte, Julian Simon, Dani Navarro, Luis Angel Mate and Nicolas Edet.
The final team spot was to be filled by either Cyril Lemoine of Kenneth Vanbilsen but in the absence of Bouhanni, both riders are now likely to be at the Grand Depart.