Israeli lawyer Ervin Eran Shahar filed the indictment on behalf of the Civil Coalition, a civil rights nongovernmental organization active in Israel and elsewhere.
German prosecutors confirmed that they had received the complaint. A spokeswoman declined further comment.
Ahmadinejad has repeatedly expressed doubt that 6 million Jews were killed by the Nazis during World War II.
Denial of the Holocaust is a crime in Germany punishable with up to five years in prison.
(Reuters)