Honda quoted Cesena’s Maurizio Bufalini hospital as saying the 35-year-old had "a serious polytrauma with subsequent serious cerebral damage".
Doctors had placed the 2006 MotoGP champion, known as "The Kentucky Kid", into a medically induced coma after the incident on Wednesday, the BBC reported earlier.
Hayden was taken to the hospital after being struck by a car while training on his bicycle along Italy's Adriatic coast following a weekend Superbike race at the Imola circuit.
Honda said he was taken initially by ambulance to a hospital near the coastal resort of Rimini before then being transferred to Cesena.
Hayden's fiancee Jackie and team members had been joined at his bedside by brother Tommy and mother Rose who flew in from the United States.
Italian media quoted the hospital as saying on Wednesday that Hayden had suffered a cerebral edema and lower body fractures and surgery had not been possible immediately because of his condition.
Italian great Valentino Rossi, who leads the championship and is racing in France this weekend, hailed his former team mate as "one of the best friends I have had in the paddock".
"Come on Nicky, we're all with you," added the 38-year-old .
Hayden last raced in the MotoGP championship in Spain in September 2016 as a stand-in for injured Australian Jack Miller at the privately-run Marc VDS Honda team. He started 216 races between 2003 and 2015, winning three.
The dangers of training on public roads have been highlighted in recent weeks by other accidents affecting professional athletes.
Michele Scarponi, the 2011 Giro d'Italia cycling champion, was killed last month after being hit by a van while training close to his home in Filottrano in eastern Italy.
Britain's Tour de France champion Chris Froome escaped unhurt this month while having his bike written off in a hit-and-run incident near his Monaco home.
(Writing by Alan Baldwin in London, editing by Richard Lough and Toby Davis)
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