In a separate incident, more than 40 people drowned after another migrant boat sank between Libya and Italy.
Almost 10,000 migrants trying to cross the Mediterranean have been rescued in recent days. Italy has called for more help from the EU to handle the crisis.
More than 500 people from Africa and the Middle East have died making the perilous crossing since the start of the year. 400 people were believed to have drowned when their boat capsized.
The 15 Muslim migrants involved in the row with Christians were arrested in the Sicilian city of Palermo and charged with "multiple aggravated murder motivated by religious hate".
The suspects, who are from the Ivory Coast, Senegal, Mali and Guinea, were among 105 migrants travelling in an inflatable boat that left Libya.
Eyewitnesses told police how the altercation resulted in Christians being thrown overboard, and that some of the survivors had formed human chains to avoid a similar fate.
Also, the Italian navy plucked four survivors - a Ghanaian, two Nigerians, and a man from Niger - from the sea. They said their inflatable boat had sunk after leaving Libya with 45 people on board.
The International Organization for Migrants (IOM) says the missing 41 people have drowned.
The four survivors were taken to Sicily along with 600 other migrants trying to make the crossing in various vessels.
Earlier on Thursday Italian Foreign Minister Paolo Gentiloni said Italy had "not had an adequate response from the EU" about the migrant crisis.
But European Commission spokeswoman Natasha Bertaud said the organisation had no "silver bullet" for the problem.
Last year a record 170,000 people fleeing poverty and conflict in Africa and the Middle East made the perilous crossing to Italy.