The human rights watchdog cited 24 claims of abuse this year as police tried to force migrants to get fingerprinted in Italy. It also reported the deportations of some asylum-seekers to war-torn countries like Sudan without proper checks on their safety.
The head of immigration at Italy's interior ministry dismissed the report's findings.
"It is totally false that the police are violent with the migrants," Mario Morcone was quoted as saying by news agency ANSA.
The allegations come as Italian authorities try to implement new EU rules adopted last year on how to handle migrants and asylum-seekers. This includes fingerprinting them in the first EU country they arrive in, so they can be processed and, if granted asylum, relocated to another EU state according to migrant-sharing quotas.
Many migrants, however, want to travel to a specific country, often to reach relatives, and resist fingerprinting.
"In their determination to reduce the onward movement of refugees and migrants to other member states, EU leaders have driven the Italian authorities to the limits - and beyond - of what is legal," said Matteo de Bellis, Amnesty International's researcher on Italy.
Amnesty International said while the behavior of most police remains professional, the findings show a need to independently review the EU rules.
The report was based on interviews with 170 migrants. Of the 24 claims of physical abuse, 16 were of beatings as police tried to force migrants to get fingerprinted. A 16-year-old boy and a 27-year-old man claimed police sexually humiliated them and inflicted pain to their genitals.
Another issue was deportations to countries where the security of the asylum-seekers couldn't be verified.
Italian and Sudanese authorities signed a deal in August allowing for identification of the asylum-seekers after they have been expelled from Italy. The procedure raises risks of human rights violations upon their return, Amnesty said.
About 40 people identified as Sudanese nationals were put on a plane to the country from Italy. There was at least one claim of beatings upon their return.