It says the accident occurred near the French Mediterranean port of Marseilles on Wednesday as the Cypriot-owned Louis Majesty was sailing from Barcelona to Genoa in Italy with 1,350 passengers and 580 crew.
The victims were only identified as a German and an Italian man.
Louis Cruise Lines spokesman Michael Maratheftis said the ship was hit by three "abnormally high" waves up to 26 feet (8 meters) high that broke glass windshields in the forward section. It is heading back to Barcelona.