The Marussia driver suffered a "severe head injury" after being involved in a collision on turn seven of lap 43 at the Suzuka circuit on Sunday.
The incident occurred in the same place where Adrian Sutil had spun out shortly before, with Bianchi hitting a recovery vehicle that was dealing with the Sutil situation.
After being removed from his car, Bianchi was taken to a Mie General hospital while still unconscious.
An update on his condition was subsequently released by Formula One's governing body, the FIA, who confirmed he would be moved to intensive care after undergoing surgery.
"On lap 42, Adrian Sutil lost control of his car, spun and hit the tyre barrier on the outside of turn seven," an FIA spokesperson said.
"The marshals displayed double waved yellow flags before the corner to warn drivers of the incident. A recovery vehicle was despatched in order to lift the car and take it to a place of safety behind the guardrail.
"While this was being done, the driver of car 17, Jules Bianchi, lost control of his car, travelled across the run-off area and hit the back of the tractor.
"Once the marshals reported that the driver was injured, medical teams were despatched and the safety car was deployed. These were followed by an extrication team and an ambulance.
"The CT scan shows that he has suffered a severe head injury and is currently undergoing surgery.
"Following this, he will be moved to intensive care where he will be monitored.
"Mie General hospital will issue an update as soon as further information becomes available."
With Bianchi's father, Philippe, suggesting to television station France 3 that it will be at least 24 hours before more information is known on his son's condition, fellow drivers and former F1 stars were quick to show their concern for the 25-year-old Frenchman.
McLaren's Jenson Button, who finished fifth, tweeted: "My thoughts are with fellow driver Jules Bianchi. The whole of the Motorsport world is pulling for you. #F1family ForzaJules".
And four-time F1 world champion Alain Prost took to his personal Twitter account to post: "I am thinking of you a lot, @ Jules_Bianchi".
Addressing television reporters immediately after the race, winner Lewis Hamilton admitted that his victory had been overshadowed by the incident.
"It's a real anti-climax to hear that another driver has been seriously injured," he told Sky Sports.
"I couldn't see what was going on and I really hope he's okay."
Mercedes team-mate Nico Rosberg, who finished nine seconds behind Hamilton in second, was also praying for Bianchi to make a speedy recovery.
He tweeted: "My thoughts are with our colleague Jules and his family and team-mates, and we are hoping for some positive news. #japaneseGP".
