If they're between ages 7 to 16, their parents will face a fine.
Unvaccinated children are now banned from attending preschool in Italy, as a new law came into effect this week.
The deadline for parents to provide proof of vaccination was on Monday, according to news reports.
The city of Bologna reportedly has at least 300 children who now do not comply with the vaccination requirements and are at risk of suspension from school.
After months of heated debate, a law in Italy has finally entered into force, mandating that children must be vaccinated to be accepted into school.
But in a reversal of policy, the coalition fell into line with mainstream medical opinion and insisted that as of this week, children attending school must receive immunisations for a range of infectious diseases, including measles, mumps, rubella and polio.
"Italy's measles vaccine coverage was par with Namibia, lower than Ghana", San Raffaele University in Milan microbiology and virology professor Roberto Burioni told CNN previous year.
"Now everyone has had time to catch up", Health Minister Giulia Grillo told La Repubblica. However, the B.C. government has said that it is only planning to require mandatory reporting of vaccination status in the upcoming school year.
According to the BBC, Italy has fallen behind other countries in terms of vaccination rates.
Across the world, health authorities are grappling with a global resurgence of measles, with record numbers recorded in Europe and deadly outbreaks in the Philippines and Madagascar.