"There's a risk not only of massive illegal immigration, but also of terrorist infiltrations," the commander in chief of the Italian navy, 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.
More than 66,500 migrants have arrived in Italy from North Africa this year so far, from where most hope to reach other destinations in Europe. 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.
Such threats may come from "cultures soaked in fundamentalism, like Mali", while "in Somalia there is an al-Qaeda movement which is stronger and more dangerous than in Afghanistan," he said.
While he said over 180 traffickers had been arrested since the operation began last October, Binelli Mantelli did not say whether anyone had been arrested on suspicion of "terrorist" activities.
Between 60 to 70 percent of those arriving by boat were asylum seekers escaping warzones, "often engineers, doctors, lawyers...men, women and children fleeing for their lives", while the rest were economic migrants, he said.
The admiral's warning of "terrorist infiltration" came as the United States and Britain upped security checks at airports amid fears extremist Muslim groups are making new explosives that would evade standard checks.