The Italian coast guard says migrants have been arriving at an unprecedented rate since last Friday, with 10,000 pulled from rickety vessels at sea and another 400 people drowned off Libya.
According to reports, 15 men have been accused of "multiple aggravated murder motivated by religious hatred," police said in a statement.
The police said those arrested were Muslims while those thrown overboard were Christians.
The 12 victims were reportedly Nigerians and Ghanaians, while the 15 suspects came from Senegal, Mali and Ivory Coast.
Distraught survivors, who set off from Libya on Tuesday before being rescued by an Italian vessel on Wednesday, told a "dreadful" story of "forcefully resisting attempts to drown them, forming a veritable human chain in some cases", police said.
Itayi Viriri from the International Organisation for Migration told Premier: "We've not really seen a situation whereby this kind of incident occurs where maybe people are targeted because of their religion - all we can say for now is we have to wait for the investigators to finish their work, and then we'll find out exactly what happened.
"If proven to be the case, it certinately would be a new and very, very worrying dimension of this already very periless journey that these migrants have to take."
John Pontifex is from Aid to the Church in Need, he told Premier's News Hour: "This was not happening in this way 15 years ago or perhaps 10 years ago, or even five years ago - and yet now it's a really grave phenonmanan, that extremisits have in their sights Christians.
"Indeed they have Muslims of different stripes and colours in their line of fire too - but Christians in particular seem to be becoming under increased attack.
And as a result of that, we at Aid to the Church in need, and other organisations are deeply concerned - I was in northern Nigeria two years ago and I saw for myself the extent of the violence that's been perpretrated against Christians and it was a shock to behold."
Listen to Hannah Tooley speak to John Pontifex from Aid to the Church in Need here:
