"It has emerged from the tales of the survivors of the October 3 wreck that all the women were raped by the members of the criminal organization that ran the migrant trafficking," officer Corrado Empoli said in a report from ANSA.
The report did not say how many women were raped.
The vessel sank off the island of Lampedusa. The migrants were from Africa, seeking a safe haven in Europe, authorities said.
One of the suspects, Mouhamud Elmi Muhidin, 34, was identified when the survivors of the shipwreck attempted to lynch him, ANSA reported.
He is accused of kidnapping, trafficking human beings, conspiracy to commit crimes aimed at illegal immigration and sexual violence.
The other suspect, Attour Abdalmenem, was charged with favoring illegal immigration.