Italian police have arrested a group of Muslim migrants who allegedly threw 12 Christians overboard in a religious hate-fuelled mass murder while crossing the Mediterranean.

The 15 arrested people were on a boat from Libya crammed with more than 100 people by human traffickers.

They set off on Tuesday in the rubber vessel as a wave of migrants took advantage of calm seas and warm weather for the treacherous journey.

During the voyage, Christian migrants from Nigeria and Ghana were allegedly threatened with being abandoned at sea by the arrested passengers from the Ivory Coast, Senegal, Mali and Guinea Bissau.

Eventually the threat was carried out and 12 were pushed overboard, who are now feared dead.

Italian police said that the victims “professed the Christian faith while the aggressors were Muslim".

The 15 were accused of multiple homicide aggravated by religious hatred, a statement added.

They may have killed more people if the surviving Christians had not managed to stay on board by forming a “human chain” to resist the assault.

Traumatised survivors told police of the row after landing in the port of Palermo on Wednesday morning.

They had been rescued at sea by the ship Ellensborg but others were not so lucky.

More than 40 people are believed to have died in a sinking earlier this week, the International Organisation of Migration said.

Four migrants rescued by the Italian Navy reported a shipwreck to aid workers after arriving in the Italian port of Trapani on Thursday.

Shipwrecked migrants sit on the deck of a rescue vessel as they arrive in the Italian port of Augusta in Sicily on April 16, 2015. (AFP/Getty Images)

The survivors, from Niger, Ghana and Nigeria, were found floating in the sea by a helicopter after spending four days adrift when their boat from Tripoli sank.

The latest tragedies come days after aid agencies reported that 400 migrants were presumed dead in the loss of another ship near the Libyan coast.

Almost 1,000 people have died crossing the Mediterranean since the start of this year, compared to just 17 during the same period in 2014.

Struggling aid agencies have blamed the end of Italy’s dedicated Mare Nostrum search and rescue mission, which was replaced by a limited and underfunded EU-wide effort called Frontex.

Migrants rest after disembarking in the Sicilian harbour of Augusta on 16 April (Reuters)

Justin Forsyth, the chief executive of Save the Children, said: “Our political leaders cannot ignore the fact that without search and rescue we are allowing thousands of innocent children and their families to drown off the coast of Europe.”

Yusuf, a 17-year-old Palestinian boy who made the deadly crossing to Italy after fleeing Gaza earlier this year, said human traffickers frequently threatened to kill desperate migrants.

“The traffickers had guns and if you talked they said they would throw you overboard or shoot you,” he told Save the Children.

Last year, more than 100 migrants were thrown overboard a boat after smoke spread through the hull, causing traffickers to stab and assault passengers at random before throwing them in the sea.

Survivors said the mass murder was carried out as hundreds of passengers surged onto the deck and they were told to stay below or suffer the same fate.