The doctor, the first Italian to be infected with the disease, was flown into the military airport of Pratica di Mare, outside the capital.
The doctor, who reports say is a 50-year-old man, was transported in a specially sealed unit on board a military plane, TV pictures showed.
He will be hospitalised at the Lazzaro Spallanzani national institute for infectious diseases.
The Italian health ministry said he has not yet developed feverish symptoms and his general condition is good.
The doctor was working for the charity Emergency at a clinic for Ebola victims when he contracted the disease, which has killed nearly 5,500 people in its latest outbreak in west Africa.