The fire brigade said two people, including a 30-year-old woman, were pulled out of the wreckage dead and some passengers were still trapped underground.
"We are working to free people who are still trapped in the metal wreckage, our aim at the moment is to save lives," fire brigade officer Luca Cari told news agency Reuters outside the station.
The accident occurred when one train arriving at the station at high speed crashed into the back of another that was still discharging passengers at the Piazza Vittorio underground station in the city centre.
It occurred at 9.47am local time, at the crowded station. Unconfirmed early reports said the driver of the second train did not stop at a red light.
A witness said overhead beams of the station collapsed when the train rammed into the rear of the other which was stationary with its doors still open.
"About one quarter of the first carriage of the train I was on was totally crushed," a man identified only as Fabiano told Sky Italia TV.
"All the lights went out. It was frightening," another man who had been on one of the trains told Sky from the scene.
Live footage showed police and other rescue workers carrying injured passengers from the station.
Witnesses said people spattered with blood were leaving the station while others were still trapped down below There were also reports that an electrical panel exploded when the trains crashed.