The 53-year-old was involved in a crash with a lorry in Pienza on Friday.
Zanardi was taken by helicopter to hospital in Siena, where he is on a ventilator in intensive care.
“The operation went as it should have, it was the original situation that was not good,” Zanardi’s surgeon said.
“What the prognosis will be tomorrow, in a week, in 15 days, I don’t know.
“Serious means he’s in a situation where he could die, in these cases improvements can be very small over time and worsening can be sudden.”
The hospital had previously said “the neurological picture remains serious” following an operation that lasted almost three hours.
Zanardi had both legs amputated after crashing in the American Memorial 500 Cart race at Lausitz, Germany, in 2001.
He has since become a four-time Paralympic handcycling gold medallist.
“You have never given up and with your extraordinary fortitude you have overcome a thousand difficulties,” Italian prime minister Giuseppe Conte said on Twitter.
“Come on Alex Zanardi, don’t give up. All of Italy is fighting with you.”
Former Formula 1 world champion Mario Andretti tweeted: “I am so anxious and frightened about Alex Zanardi that I’m holding my breath. I am his fan. I am his friend.
“Please do what I’m doing and pray, pray for this wonderful man.”
Zanardi was taking part in an event called the Obiettivo Tricolore, a journey where the participants ride across Italy on handbikes, cycles or wheelchairs. (Courtesy BBC)