Prosecutors accuse the two of causing the shipwreck, murder and aiding illegal immigration.
They said the two sabotaged the boat's engines in order to then request assistance from Italian authorities.
Their action apparently damaged the boat itself, which began taking on water and caused it to capsize when the migrants ran to one side to avoid falling into the sea.
The incident happened on Monday some 150 kilometres (93 miles) south of Italy's southernmost point, the island of Lampedusa, and 80 kilometres north of Libyan shores.
Pope Francis spoke of the tragedy at his general audience in St Peter's Square, telling a crowd of faithful: "We need to give priority to human rights and join forces to prevent these shameful massacres".
The victims included 12 women and two young girls.
Their bodies and the survivors arrived in Sicily on Tuesday on board an Italian warship that aided in their rescue, along with coast guard and merchant vessels.
Immigration campaigners estimate that some 20,000 migrants have died making the perilous crossing of the Mediterranean in rickety boats in the past 20 years.