The investigation targets in particular two capital increases that the Hessen and Rheinland-Palatinate regional authorities participated in and a profit-and-loss transfer agreement with its mother company Fraport.
The commission, Europe's top competition watchdog, said it would also look into fees at the airport and in particular individual contracts with Ryanair. German airline Lufthansa has complained in the past that Ryanair benefited from reduced fees at the airport, where the cut-price airline has one of its biggest European hubs.
Hahn is situated around 150 kilometres southwest of Frankfurt and is one of Ryanair's biggest European hubs.
Flughafen Frankfurt-Hahn GmbH is 65 percent owned by Frankfurt airport operator Fraport, while the regional state authorities of Hesse and the Rhineland-Palatinate each hold 17.5 percent.