A Swedish coastguard ship docked at the Sicilian port of Palermo on Thursday carrying more than 570 migrants and the bodies of 52 people, officials said.
The Italian coast guard said it had rescued around 1,400 people off the coast of Libya on Thursday, 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.
Shortly after the bodies were brought ashore, Libya's coast guard announced that another boat, carrying around 200 migrants, had capsized off the country's coast. At least 10 people drowned in that incident. The search for survivors was ongoing.
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Swedish officials said the Poseidon coastguard vessel had rescued 130 people Wednesday from a rubber dinghy and another 442 people from a wooden boat found drifting off the Libyan coast.
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 told AFP.
He said only one survivor was pulled unconscious from the hold and flown to an Italian hospital for treatment.
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.