The boat was capsized on Sunday off the Libya coast.
The arrested Captain and crew members were among 27 survivors who arrived in Sicily late on Monday. They were arrested on suspected charges of human trafficking.
Both were arrested after European Union (EU) announced measures to address migrant crisis in the Mediterranean.
Search and rescue operations will be intensified and there will be a campaign to destroy traffickers' boats.
A homicide investigation has been opened into the disaster, said Italian Infrastructure Minister Graziano Delrio.
About 800 people died in Sunday's boat sinking tragedy, announced UN refugee agency. Earlier death toll was announced 700.
UN Secretary-General Ban Ki-moon on Sunday called for a "comprehensive and collective" response to ensure "a robust search and rescue capacity in the Mediterranean after a boat capsize off the Libyan coast.