The two were among only 28 survivors after a boat capsized and left 800 migrants dead, including children. The arrests follow widespread criticism of the EU's handling of the migrant crisis in the Mediterranean.
The UN confirmed the death toll of 800 on Tuesday that included Syrians, Eritreans and Somalians leaving from Libya. Since the incident EU ministers ramped up its measures to target human traffickers and improve search and rescue efforts in the Mediterranean.
Initially the union had cut down its operations last year in efforts to try to discourage migrants, but escalated conflict in the region and spring weather have driven more people to leave.
One of the EU's measures is to destroy boats belonging to human traffickers. Italian officials said the Tunisian and a crew member were also charged with favoring illegal immigration.
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