Bianchi was taken to hospital by ambulance, still unconscious, after colliding with a recovery vehicle which was attempting to lift Adrian Sutil's Sauber away from danger after the German himself had skidded into a wall on lap 42 at Suzuka.
The FIA said that Bianchi would continue to be monitored in intensive care following his operation.
"The driver was removed from the car, taken to the circuit medical centre and then by ambulance to Mie General Hospital," FIA press officer Matteo Bonciani 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."
The FIA added: "A recovery vehicle was despatched in order to lift (Sutil's) 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."
"Jules is seriously injured," Bianchi's father Philippe told France 3 television. "He is undergoing surgery for a head injury and we will need to wait 24 hours to know any more on his condition."Bianchi, a member of Ferrari's young driver programme, is in his second season in Formula One.
He scored a memorable ninth place in Monaco this year, giving the back-of-the grid Marussia team their first points since their debut in 2010.
Championship leader Lewis Hamilton won Sunday's race, which had been threatened by a typhoon and began behind the safety car with drivers complaining over team radios that they were unable to see through the spray.
Starting in second behind Mercedes team-mate Nico Rosberg, Hamilton had radioed: "Tell Nico not to do anything dramatic because I can't see him."
Sutil witnessed Bianchi's shunt 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. Hopefully he is in good hands."
The safety car and medical car were sent out and the race brought to a premature halt, giving Hamilton his eighth victory of the season, although the Briton's celebrations were muted as news of Bianchi's accident filtered through.- 'All concerned' -
"We're all very concerned about our colleague, Bianchi," said Hamilton.
"I don't really know what to say. Obviously (the race) didn't finish the way we would have hoped but really, my prayers are with him and his family."
German Rosberg, who finished second, said: "I'm not thinking about the race -- I'm thinking about my colleague. I'm hoping for the best."
Williams driver Felipe Massa, who was involved in a serious crash during qualifying for the 2009 Hungarian Grand Prix, said: "We need to understand what has happened with Jules. I'm very worried.
"I was already screaming on the radio five laps before the safety car that there was too much water on the track, but they took a bit too long and it was dangerous. So we saw that there were some crashes at the end."
Reigning world champion Sebastian Vettel, who was third on Sunday behind the Mercedes duo of Hamilton and Rosberg, said results were irrelevant in the light of Bianchi's crash.
"Everything that happened with the racing on track is secondary today, one of us is in a bad shape and we don’t yet know how he is," said the German Red Bull star.
"Jules had a bad accident and we hope to have some very good news, very soon. Not knowing what’s going on feels terrible, I think all the drivers really feel with him, as we know how difficult and slippery it was today; we hope for the very best."
Formula One has been relatively free of bad crashes in recent years following safety-improving measures that were implemented in the wake of the last fatality to hit the sport - that of former world champion Ayrton Senna at the 1994 San Marino Grand Prix.
Marussia reserve driver Maria De Villota lost her right eye in a test crash in July 2012.
The 33-year-old Spaniard was found dead in a Seville hotel room in October 2013.
There was an out-pouring of sympathy for Bianchi from within the sport and outside.
"#CourageJulesBianchi..hoping to read good news of your recovery soon," tweeted France's former Wimbledon tennis champion Marion Bartoli.