"The remarks are unforgivable and we will ask our lawyers to look into the matter," Deutsche Bahn said in a statement.
Michael Szentei-Heise, the leader of the Jewish community in the western city of Düsseldorf, was quoted by the Rheinischer Post newspaper as saying Mehdorn was a "a Nazi at heart".
"If Mehdorn had held the same position in the Third Reich he would have arranged the deportation of Jews with great conviction," he added.
The remarks came amid a debate over Deutsche Bahn's decision to charge transport fees to the organizers of a travelling exhibition in memory of Jewish children deported in the Holocaust during World War II. The exhibition traces the plight of, among others, 11,400 Jewish children who were deported from France to the Auschwitz death camp, often crammed together in cattle trucks, between 1942 and 1944.
The Nazi regime paid Deutsche Bahn's wartime predecessor, the Reichsbahn, 25 Reichsmarks, the equivalent of €25 ($38), for each child it transported to the camp.
Deutsche Bahn initially refused to host the exhibition in stations, saying that the subject deserved more than the divided attention of hurried commuters, but relented after its stance drew strong criticism.
The exhibition opened in Berlin in January and is being shown at eight other stations in Germany.