Marini had travelled to the Suzuka Circuit after the British Grand Prix that was held over the weekend and the Italian was testing Honda's bike for the Suzuka 8-Hour endurance race when he crashed heavily on the second day of testing.
"Suffering from a dislocated left hip, damage to the ligaments in his left knee, fractures in the sternum and left collarbone and a right-sided pneumothorax, Marini was transferred to local hospital and stabilised," Honda said.
"Marini will remain under observation in Japan until he is deemed fit to travel."
Honda did not give a timeline for Marini's return. The 27-year-old is 13th in the MotoGP riders' standings after seven rounds.
The next MotoGP round is the Aragon Grand Prix in Spain on June 7-8.