"There's a risk not only of massive illegal immigration, but also of terrorist infiltrations," Luigi Binelli Mantelli told La Stampa.
He said that police boarding migrant boats intercepted by the navy were trained in special interrogation techniques designed to root out traffickers and potential "terrorists".
"There are indicators which confirm contacts between traffickers (who organise the boats) and terrorists," he said.
Italy's "Mare Nostrum" ("Our Sea") operation is not just tasked with rescuing immigrants -- thousands of whom have drowned on the perilous crossing -- but is also "monitoring the sea in a situation of international crisis", he said.
The majority come from Eritrea, Syria, Somalia and Mali.
As well as "operative terrorists", there are "latent terrorists... Who present themselves as asylum seekers", Binelli Mantelli said.