The investigation had targeted national operator ITA Airways as well as budget airlines easyJet, Ryanair and Wizz Air.
Antitrust official Guido Stazi told parliament the regulator had found no evidence to conclude that prices of flights last December had been determined by "illicit coordination" among airline operators.
He said the airlines had already been informed of the findings and the case would be closed formally within the next few weeks.
The investigation followed a complaint by consumer group Codacons and looked into flights connecting the Sicilian cities of Palermo and Catania with places including Rome, Milan, Turin and Bologna.
The issue of the high price of flights to the islands of Sicily and Sardinia flared again over the summer when the Italian government responded initially with a plan to cap fares.
The government changed course after protests led by Ryanair, the market leader in Italy, and asked the antitrust body to police prices.
(Writing by Keith Weir; Editing by Gavin Jones and David Goodman)