The 25-year-old's Marussia collided with a recovery vehicle after German Adrian Sutil had skidded into a wall on lap 43 at Suzuka.
"The driver is not conscious, he has been sent to the hospital by ambulance because the helicopter cannot go in these conditions," said Formula One's governing International Motoring Federation (FIA) presser officer Matteo Bonciani.
"For the moment, we cannot say anything (more)."
The safety car and medical car were sent out and the race red-flagged, giving Lewis Hamilton his eighth victory of the season, although the Briton's celebrations were muted as news of Bianchi's accident filtered through.
The race had been threatened by a typhoon and began behind the safety car due to torrential rain, with Hamilton and several drivers complaining they could not see through the spray.
Sutil witnessed Bianchi's shunt at the Dunlop corner after going out himself.
"I had a spin and ended up in the wall," he said. "I stood up and they tried to rescue the car. Jules was in the same area and lost the car. I have no more information. We are all aware of the situation. Hopefully he is in good hands."
German Nico Rosberg, who finished second behind Mercedes team-mate Hamilton, said: "I'm not thinking about the race — I'm thinking about my colleague. I'm hoping for the best."