Bianchi, 25, was unconscious as he was taken to hospital following the incident which brought the rain-affected race to an early conclusion.
He lost control at the same spot on the Suzuka circuit where recovery vehicles were attending a previous crash.
In wet conditions, Sauber driver Adrian Sutil firstly spun and hit the tyre barrier as rain intensified in the latter stages of the race.
While recovery vehicles were lifting Sutil’s car, Bianchi “lost control of his car, travelled across the run-off area and hit the back of the tractor”.
The race was red-flagged and then declared over after 44 laps.
“The driver was removed from the car, taken to the circuit medical centre and then by ambulance to Mie General Hospital,” the FIA said in a statement.
“The CT scan shows that he has suffered a severe head injury and he is currently undergoing surgery. Following this he will be moved to intensive care where he will be monitored.”