German, Israeli and Bavarian flags were lowered to half-staff at the beginning of Wednesday's ceremony at the Fuerstenfeldbruck air base, outside Munich.
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Representatives of both the German and Israeli governments attended the ceremony as well as the victims' families and the surviving athletes.
Speaking at the ceremony Vice Premier Silvan Shalom said: "Terror does not differentiate between women and men, adults and children….terror groups try to hurt Israelis and Jews, they tried and succeeded at the Olympics…just recently in Burgas Bulgaria a terrorist murdered Israelis and proved the brutality of terror."
Minister Shalom also mentioned the attempted terror attacks against Israeli targets in Thailand among others.
"The writing for these activities is on the wall, and it is aimed at Iran. Iran denies the Holocaust and delegitimizes Israel. Iran is not just an Israeli problem…terror can hit anywhere and anyone."
"The historic occasion we are marking today states clearly that Germans and Israelis do not forget the past," the vice premier added.
"It was a brutal massacre…there are still many questions regarding the events of 40 years ago. After the Olympic committee refused to hold a moment of silence at the games (London Olympics) I wish to thank the Germans who asked the committee to commemorate the victims," Shalom concluded.
Speaking at the ceremony, widow of slain Israeli athlete Andre Spitzer, Ankie Spitzer mentioned the secret documents relating to the events of the massacre which were published by the State Archives last week: "I demand that the German authorities publish all documents and reinvestigate the fiasco of the release of the kidnapped (athletes)."
The attack began on Sept. 5, 1972, when terrorists slipped into the unguarded Olympic Village in Munich, seized the Israeli compound and demanded the release of jailed comrades.
By the time the violence ended at Fuerstenfeldbruck the following day, 11 Israelis and one German police officer were dead.
AP contributed to the report
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