Police, firefighters and local officials arrived at the Pessina di Ostuni elementary school shortly after the incident and the victims were transported to hospital with head injuries, La Stampa reported.
The incident happened just months after the school, which has 800 pupils, opened following years of renovation works.
"Their condition is not severe," Gianfranco Coppola, the city's mayor, was quoted in La Stampa as saying after visiting the children in hospital, although he added that doctors were carrying about more tests.
A teacher was also injured, Il Fatto Quotidiano reported.
According reports, a layer of plaster, measuring about an inch, fell down from the ceiling, hitting the two seven-year-olds on the head.
The school had re-opened in January after four years of renovation works.
This isn't the first incident of a school ceiling collapsing in recent times. In January, seven children were injured after plaster fell from the ceiling at their nursery school in Milan.
READ MORE: Seven kids hurt in Milan classroom accident