Some 100 refugees had occupied the square, close to the city’s main train station, since Saturday after they were evicted from an adjacent office block where they had been living for about five years.
Images showed police dressed in riot gear clashing with some of the refugees and firing water cannon to try to disperse them at the Indipendenza square on Thursday morning.
A man, who appeared to be walking with the aid of crutches, was pictured raising his arms to his face as water was sprayed towards him.
Another image showed a woman lying on the ground being given medical treatment by a doctor after she was hit by the water.
The square was strewn with mattresses, overturned rubbish bins and broken plastic chairs.
Up to 800 squatters had been living in the office building.
Hung on the building was a sheet with writing reading “We are refugees, not terrorists” in Italian.
A small fire burned on the pavement and a sheet hanging from a first-floor window was set alight by the few remaining squatters inside.
Most of the squatters were Eritreans and Ethiopians who had been granted asylum. Police said they had refused to accept lodging offered by the city.
In a statement, the police said the refugees had gas canisters, some of which they had opened, and officers had been hit by rocks, bottles and pepper spray. Two people were arrested.
Officers said the use of hoses were necessary because of the risk presented by the presence of cooking gas canisters and other flammable materials in the piazza surrounded by the apartment buildings.
The operation to clear the migrants from the piazza is among four major evictions since July conducted as a security measure, officials said.