Libya has long been a popular gathering point from where thousands of African migrants have set sail to cross into Europe via Lampedusa off the southern coast of Sicily.
A deal between Gaddafi and Italy to send migrants back before they entered Italian waters curbed the flow of migrants -- until the Libyan uprising earlier this year brought down strict border controls and drew a fresh wave of migrants.
Italy, once Gaddafi's biggest ally in Europe, turned into a target of his rage after the former colonial power endorsed the Libyan rebel movement and joined a NATO campaign to oust the veteran leader, Frattini said.
"We have terrible messages [in our possession] and they will be made public soon," Frattini said in an interview with Avvenire, the Italian bishops' newspaper.
"We have proof of orders given by Gaddafi's government to transform Lampedusa into an inferno: 'Put thousands of desperate people on boats and throw the island into chaos.' We have proof and we can't ignore it."
Italy also has "messages" showing that Libyan authorities ordered civilian clothes be put on the bodies of soldiers, so as to pin blame for their deaths on NATO, he said.
Since the uprising started, tens of thousands of migrants have arrived in Lampedusa, almost overwhelming the tiny island, which was unprepared for the sudden deluge.
Chaos on the island turned into a massive headache for Prime Minister Silvio Berlusconi's conservative government, which came to power in 2008 pledging to stop illegal immigration.
Italy has taken in as many as 50,000 migrants since the start of the year, Frattini told Italian radio.
The orders to put migrants on boats to Italy were given by Gaddafi himself, Libya's ambassador to Italy, Hafed Gaddur, who defected to the rebel side in February, told Italian radio.
Hundreds of people have drowned attempting the dangerous crossing from North Africa to Lampedusa since the fighting started in Libya in February.