Marquez suffered a highside at the Turn 5 left-hander at the end of the first qualifying segment.
The 27-year-old immediately threw off his right glove and took some time to get to his feet, before needing to be helped away by the marshals.
Despite progressing into Q2, Marquez was unable to compete in the session as he was taken to the medical centre for checks.
Initial examination discovered potential rib fractures before he was taken to a hospital in New Delhi for further checks.
Scans ruled out any serious injury, but he has suffered fractures to his sixth, seventh and eighth ribs on the left side of his body.
This has forced him out of Saturday’s sprint at the Indian GP and Sunday’s main race.
And with the Japanese Grand Prix just a week away, it is likely Marquez will also be absent from the Motegi round.
Source: Autosport