ROME — Migrants in a Rome piazza threw rocks, bottles, and gas cans at riot police using water cannons to clear out about 100 mostly Ethiopian and Eritrean asylum-seekers early Thursday as part of a security operation harshly criticized by humanitarian groups.

At least two people were detained, and 13 were injured.

The dawn operation came days after authorities cleared most of the 800 migrants who had been squatting in an adjacent building since 2013.

Police said in a statement the operation was necessary because the migrants remaining in the piazza had refused to accept city-organized lodging and because of the risk of cooking gas canisters and other flammable materials.

Authorities have said such raids to clear migrants from buildings and squares, at least four since July in Rome, are part of anti-terrorism measures.

Asylum-seekers, mostly women and children, who had been allowed to remain temporarily in a nearby building hung signs out of its windows saying ‘‘We are not terrorists,’’ as some threw canisters into the street. They were also cleared out, and brought to a police station.

The city of Rome said in a statement that the most vulnerable among the migrants, including families with minors, and the elderly and disabled, were being given priority, and that all had been given food and drinks by authorities.

The statement said workers had run into resistance in recent months to conduct a census of migrants living in the structure and piazza.

The UN refugee agency, UNICEF, and humanitarian organizations have protested Italy’s moves, saying they were carried out without warning and that there isn’t enough adequate housing for them and the hundreds more vulnerable asylum-seekers sleeping on Rome’s streets. They also noted that many families would be separated by the new housing arrangements and children would be uprooted from schools.