An Italian coast guard vessel arrived in Sicily on Wednesday carrying almost a thousand migrants.
The landing came as another ship, the Aquarius was headed for Spain after Italy refused to let that vessel dock with some 600 migrants on board.
The Diciotti was carrying the bodies of a woman and a teenage boy who had apparently died trying to get across the Mediterranean to Europe.
Thirteen of the other migrants who disembarked in Catania were pregnant while over two hundred are minors.
During the voyage to Sicily, four pregnant women and a man suffering from fever were evacuated urgently and taken to hospitals.
The migrant policy adopted by Italy's new government has sparked a war of words with France that exposed EU tensions over immigration.
Early in the morning, the Italian Foreign Ministry summoned the French ambassador after President Emmanuel Macron denounced the decision to block the Aquarius, saying that under international law Italy should have taken the migrants in.
Matteo Salvini, Italy's new interior minister and head of the far-right League, has said his decision not to accept the migrant boat is aimed at forcing other European states to help bear the strain.