“A few dozen” pre-school pupils in Cagliari, on the southern island of Sardinia, were forbidden from attending class after not receiving the vaccinations.
In the town of Elmas, around 40 children were reported for failing to comply with the compulsory law on vaccinations.
Another four cases were reported in Milan, where five or six more children failed to produce certification but had been absent since the end of last week due to the flu.
Meanwhile, four more children were sent home from a school in Sulmona, in the central Italian region of Abruzzo.
Some parents claimed they had not had time to get their children vaccinated before the deadline, while at least two of the cases in Sulmona involved parents who refused vaccinations out of fear of alleged side effects.
Under the new law, all children who enrol at a state nursery or school must have received shots against at least ten diseases.
The Health Ministry had warned that all children aged six or under who hadn’t had the vaccinations by March 10, and had not made an appointment to get them, would not be allowed to attend school.
Children sent home on Monday will be readmitted as soon as they have been vaccinated, according to local officials.
Italian news agency ANSA reported that around 30,000 children across Italy hadn’t received all ten vaccinations by last week.
However, the country's Higher Institute of Health (ISS), said that Italy has achieved the goal of population immunity for some diseases and is making good progress towards it for others.
More than 95 per cent of children have received the combined vaccine that protects against six common diseases including tetanus, diphtheria, hepatitis B and polio, according to the head of the institute’s department of infectious diseases, Giovanni Rezza.