Forty-one more deaths were reported in a separate incident.
Police in the Sicilian capital Palermo said they had arrested the men, from Ivory Coast, Mali and Senegal, after survivors reported they had thrown 12 people from Nigeria and Ghana to their deaths and threatened other Christians.
The 15 were arrested on charges of multiple homicide motivated by religious hatred.
“The motive for the resentment was traced to their faiths,” police said. “Twelve people are said to have drowned in the waters of the Mediterranean, all of them Nigerian and Ghanaian.”
The survivors’ account underscores the rising chaos in the Mediterranean, which thousands of migrants, many fleeing war and deprivation in Africa, try to cross in rickety boats in the hope of a better life in Europe.
Around 20,000 migrants have reached the Italian coast this year, the International Organisation for Migration (IOM) estimates, fewer than arrived in the first four months of last year, but the number of deaths has risen almost nine-fold.
Almost 450 people are now thought to have died this week after rescued migrants brought to the Sicilian port of Trapani on Thursday said 41 others travelling with them had drowned.
About 400 died earlier this week when passengers crowded to one side of their boat, causing it to capsize, survivors said.
Traffickers take advantage of a breakdown of order in Libya to charge some $1,000 for every migrant to whom they give a passage. Some also turn violent, threatening coast guards with machine guns to avoid having their boats confiscated.
The murder suspects were among almost 100 migrants brought to Palermo on Wednesday. The arrests were made on the basis of testimony from about 10 survivors, who said they had left Libya in a rubber boat on Tuesday, police said.
Italy phased out a dedicated maritime search and rescue operation called “Mare Nostrum” or “Our Sea” late last year, making way for a European Union border control mission.
The EU operation, called Triton, has been criticised by humanitarian groups and Italian authorities as it has a much smaller budget and a narrower remit than Mare Nostrum.