Formula One's governing body said the 25-year-old lost control of his Marussia on the wet track, travelled across the runoff area and hit the rear of a recovery tractor which was trying to remove a stricken Sauber.
The accident led to the race at Suzuka being stopped and cast a pall over the paddock with drivers shocked at what had happened.
McLaren's Jenson Button, who finished fifth, said it was "an accident that you hope never happens in Formula One".
Bianchi, extracted unconscious from the car, was taken by ambulance to Mie General Hospital where he underwent surgery.
"The CT scan shows that he has suffered a severe head injury," the International Automobile Federation (FIA) said in a statement.
Speaking to France 3 television, Bianchi's father Philippe said it could take 24 hours before the situation became clearer.
The accident was the most serious involving a driver at a grand prix weekend since Brazilian Felipe Massa suffered near-fatal head injuries in Hungary in 2009 after being hit on the helmet by a bouncing spring shed from a car in front.
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God loves him, lucky to come out alive, really gasly
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