The Italian coast guard said it had rescued around 1,400 people off the coast of Libya yesterday, a day after it pulled another 3,000 to safety from the same area.
Italian media said a refrigerated lorry was waiting at the dock to take away the bodies for examination by forensic experts.
Palermo's prosecutor opened a murder inquiry similar to that launched by Catania earlier this month after the discovery of 49 bodies in the hold of another packed fishing boat.
Swedish officials said the Poseidon coastguard vessel had rescued 130 people on Wednesday from a rubber dinghy and another 442 people from a wooden boat found drifting off the Libyan coast.
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They said 52 people had been found dead in the hold of the wooden boat.
Many of the bodies found were at the bottom of the hold, lying face down in water, while other bodies were underneath them, completely submerged, Dr Simon Bryant said.
Since the start of the year, more than 107,000 migrants have landed on Italy's shores, while another 157,000 have made their way across the water to Greece, according to the Geneva-based International Organisation for Migration (IOM).
Some 2,300 have died trying to reach European shores, agency figures show.