Two Nigerian women have been arrested for the crimes of aggravated manslaughter and abusive exercise of a profession.
The mother of the child is also being investigated on suspicion for conspiracy to commit manslaughter.
The twin baby boy was undergoing a circumcision operation performed by an American citizen of Libyan origin but his twin brother narrowly survived the operation following a spell in intensive care.
The doctor alerted the authorities after the baby started to bleed excessively.
The mother of the babies was believed to be an asylum seeker from Nigeria with five other children in Nigeria.
She reportedly asked for the operation to be performed in line with Islamic traditions, despite being Catholic convert.
Many Muslim immigrants in Italy practise circumcision for cultural and religious reasons but it is not a popular practice among Italy’s Roman Catholic majority.
The operations are usually performed in backstreet surgeries and private clinics as most hospital doctors refuse to perform the surgery until the boys have reached at least age four.
Over 5,000 such operations are performed in Italy every year, with 35% being done clandestinely, according to health charity Amsi.
Operations in private clinics can cost up to 4000 euros, but can be offered for between 50 and 200 euros at backstreet surgeries.