The actor, 33, missed the Monday premiere of his movie Two Lovers after doctors told him he couldn't fly because of his illness.
"Joaquin has the stomach flu," his rep, Susan Patricola, tells PEOPLE. "He had his dog boarded, his tux in hand but couldn't even sit on the plane. He did go to the hospital to get hydrated, hoping he could get on the plane but he didn't stay there. He was so sick – and so sorry he couldn't be there with everyone."
Phoenix was due to promote his drama Two Lovers at the festival. The film's director, James Gray, told reporters Monday that Phoenix wanted to make the trip to France, but he advised him to go to the doctor.
"He wanted to come," Gray told reporters. "I said 'No, go to the doctor and see what he says.' Sadly he followed my advice and they put him in the hospital."
Gray praised Phoenix's performance, calling him "fantastic" opposite Gwyneth Paltrow.
Reporting by JULIE JORDAN and PETE NORMAN