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.
President Ahmadinejad visiting the tomb of Ayatollah Ruhollah Khomeini in October (Fars)
READEach year in Iran, the last Friday of Ramadan is celebrated as Qods (Jerusalem) Day, officially a day for expressing solidarity with the Palestinian people.
"I have been notifying the Muslims of the danger posed by the usurper Israel," Ayatollah Ruhollah Khomeini, father of Iran's Islamic Revolution, said in an August 1979 announcement. "I ask all the Muslims of the world and the Muslim governments to join together to sever the hand of this usurper and its supporters...and, through a ceremony demonstrating the solidarity of Muslims worldwide, announce their support for the legitimate rights of the Muslim people..." (more)
INTERVIEW: On December 22, 2005, RFE/RL's Radio Farda spoke with FRED ZEIDMAN, director of the U.S. Holocaust Memorial Museum in Washington, D.C. Zeidman commented on Iranian President Mahmud Ahmadinejad's anti-Israeli comments.
ARCHIVE: For an archive of RFE/RL's coverage of Iran, click here.