Omar al Gawari told Ansa that the militants will hide themselves on migrant boats.
Italy, and Rome in particular, has been a target for the militants for some time.
Several threats against the capital, the centre of the Catholic Church, have been made by the group.
"In the coming weeks, Italy will experience the arrival not only of poor African immigrants but also of boats carrying Daesh (Isis)," al Gawari, who represents the country's internationally-recognized government based in the port city of Tobruk, told the Italian news agency, adding that Malta will also be affected.
Thousands of migrants have landed in both countries in recent weeks, with people smugglers taking advantage of the chaos gripping Libya since the 2011 uprising that toppled dictator Moamer Qaddafi.
Italy's Foreign Minister Paolo Gentiloni said in February there was a serious danger of Isis fighters forging an alliance with local militias or criminal gangs engaged in a multi-sided battle for control of the north African country, which lies just 175km from the Italy's southernmost island of Lampedusa.
The EU on Monday called on the UN Security Council to back a proposal to use military force to destroy people smugglers' boats.