The victims were "of Christian faith, compared to their attackers who were of Muslim faith," police said in a statement, saying the 15 people arrested were accused of "multiple aggravated murder motivated by religious hate".
The incident aboard the rubber dinghy, which was carrying about 100 migrants, took place in the Strait of Sicily, between Tunisia and Italy.
According to a group of Nigerian and Ghanaian survivors, a fight broke out over religion, with a group of Muslim passengers threatening the Nigerians and Ghanaians after the latter - who were in the minority - declared themselves to be Christians.
"The threats then materialised and 12 people, all Nigerian and Ghanaian, are believed to have drowned in the Mediterranean," the statement added.
The 15 migrants arrested over the attack on their arrival in Palermo were from Ivory Coast, Mali and Senegal.
In a separate migrant tragedy, as many as 41 migrants were feared drowned after refugee boat sank in the Mediterranean, Italian media reported.
Four survivors reported the incident to Italian police and humanitarian organizations.