The airline announced last week that it would be cancelling up to 50 flights a day to help it reach its punctuality target for the year, sparking travel chaos across Europe.
But the statement from the Italian Competition Authority said the investigation would look at whether managerial problems were to blame, rather than "random, external" circumstances beyond the airline's control - and whether the disruption could have been prevented.
If Ryanair is found to have violated consumer rights, it could face a significant fine.
Italy has been particularly badly affected by the cancellations taking place over the next six weeks. Over 700 of the 2,000 affected flights were scheduled to depart from or arrive at an Italian airport, many of them domestic flights.
In terms of annual passenger numbers, Ryanair is the biggest airline in the country, controlling almost a quarter of the market.
All of the low-cost airline's hubs in Italy will see flights grounded, including both of Rome's airports and other major holiday hotspots such as Milan, Venice, and Palermo.
The antitrust probe will also look at the information Ryanair provided to customers regarding cancellations, refunds, and other solutions, and whether customers were misled regarding their right to compensation.
The airline was slow to publish the details of the affected flights, at first only sharing planned cancellations for the immediate week, angering travellers and consumer rights groups.
Italy's Transport Minister Graziano Delrio said earlier this week that the situation was "very serious".
"This has caused huge inconvenience for Italian residents, and we insist on the absolute respect of passengers' rights," Delrio said on Monday.
The airline said passengers whose flights are affected will be notified by email and text, and will be able to either change their flight free of charge or receive a full refund for the cost of the flight.