At least 40 migrants have died after apparently getting trapped and suffocating in the water-logged hold of a boat in the Mediterranean, the Italian navy said on Saturday.

The victims are thought to have suffocated after inhaling fumes from fuel after the boat took on water in the hold, the captain of the navy ship leading the rescue said on Italian state television.

Commander Massimo Tozzi, speaking from the ship, said that when his men boarded the migrant boat they found the dead in the hold "immersed in water, fuel and human excrement".

Tozzi said his ship, the Cigala Fulgosi, had taken on more than 300 survivors, including women and children.

Last Tuesday, up to 50 migrants went missing when a large rubber dinghy sank in the Mediterranean Sea. Nearly 2,000 have been picked up this week.

Around 200 migrants were presumed killed earlier this month off the coast of Libya when their boat capsized

The Mediterranean has become the world's most deadly crossing point for migrants.

More than 2,000 people fleeing war and poverty have died this year in attempts to reach Europe by boat, compared with 3,279 deaths during the whole of last year, the International Organization for Migration said last week.

People smugglers, mostly based in lawless Libya and charging thousands of dollars for passage, have sent more than 100,000 migrants by sea to Italy so far this year, according to an Interior Ministry tally. Italy took in 170,000 in 2014.