Migrants by the tens of thousands are braving the perilous journey across the Mediterranean this year, hoping to reach Europe and be granted asylum.
They are fleeing war, persecution and poverty in the Middle East, Africa and Asia.
"The dead were found in the hold," Cmdr. Massimo Tozzi, speaking from the navy ship Cigala Fulgosi while the rescue was still ongoing. Asked by RaiNews24 how the migrants died, Tozzi said "it appears to be from inhaling exhaust fumes."
The death toll was not yet final.
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"They are still counting the victims," Interior Minister Angelino Alfano told reporters.
Tozzi said the survivors included three children and 45 women, some of whom "were crying for their husbands (and) their children who died in the crossing."
The navy said that the survivors were later transferred to a Norwegian ship with the Frontex mission, a European effort to save migrant lives in the Mediterranean. The survivors were being brought to a southern Italian port.
The scenes, captured early Saturday by Associated Press journalists on a moonless night, came as Turkish authorities reported that 2,791 migrants have been caught in the Aegean Sea in the past five days alone, most of them Syrians.
Kos is only 4 kilometers from Turkey at its closest point, its twinkling lights at night an irresistible beacon to those fleeing war or poverty.
"We saw this boat filled up to unimaginable levels," Admiral Pierpaolo Ribuffo said.
So far, at least seven of the bodies had been transferred to the rescue vessel, which was headed toward Sicily, Ribuffo said.