EU's "hotspot" system resulted in practices of "torture" where refugees were forced to join the registration process.
Italian police have allegedly beat, sexually assaulted and used electric shocks on asylum seekers arriving in Italy by boat, in order to obtain their fingerprints, Amnesty International said in a report on Thursday.
EU's so-called "hotspots", reception centres for processing migrants, requires Italy to fingerprint the incomers on their arrival so they can be prevented from claiming asylum elsewhere.
"The European Union's pressure on Italy to 'get tough' on refugees and migrants has led to unlawful expulsions and ill-treatment which in some cases may amount to torture," Amnesty said.
The report said such treatment amounted to torture within the United Nations Convention Against Torture. It also said some people were detained arbitrarily.
The hotspot approach to receive refugees and migrants in key arrival countries like Italy was introduced in 2015, as a way to faster identify, screen and filter all newly arrived men, women and children.
Italy has become the main arrival point in Europe for people fleeing persecution and poverty in Africa, most of them crossing the Mediterranean from Libya in search of a better life.
Last year Europe saw an influx of more than one million migrants and asylum seekers fleeing war and poverty in its worst such crisis since World War II.
European law says refugees must stay in the country where they first enter the bloc, and that is determined by where they give their fingerprints. Until last year, most refugees refused to be identified and headed straight for the richer north.
"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," Amnesty researcher Matteo de Bellis said in a statement upon the release of the 2015/16 report.
"The result is that traumatised people, arriving in Italy after harrowing journeys, are being subjected to flawed assessments and in some instances appalling abuse at the hands of the police, as well as unlawful expulsions."
Amnesty said it had interviewed more than 170 refugees and migrants in Italy since July 2015. Most had not refused to give their fingerprints and reported no problems, but 24 people alleged having been subjected to ill-treatment by police.
"They gave me electricity with a stick, many times on the left leg, then on right leg, chest and belly. I was too weak, I couldn't resist and at that point they took both my hands and put them on the machine," a 16-year-old boy from Sudan told Amnesty researchers.
The report also condemned the assessment process for arrivals in the hotspots, which is aimed at selecting asylum seekers from those considered irregular refugees.
"People, often exhausted and traumatised from their journeys and without access to adequate information or advice on asylum procedures, have to answer questions with potentially profound implications for their futures," it said.
Over the past three years more than 470,000 refugees, mainly from sub-Saharan Africa, have reached Italy by boat. Thousands have also died while making the dangerous crossing, including at least 3,750 this year alone.