Italy’s pharmaceutical watchdog AIFA said the suspension of Fluad was a precautionary measure.
The victims were two elderly women and an elderly man, according to Italian media reports.
Novartis said “no casual relationship to the vaccine has been established”.
A review of the two batches “have confirmed that they are in conformity with all production and quality standards,” the company said.
It added that Fluad had been used since 1997, during which time more than 65 million doses have been successfully administered around the world.