The Council said its representatives would not attend a speech by President Horst Koehler for the anniversary of the liberation of Auschwitz concentration camp as they had not been greeted personally and had been treated merely as "onlookers."
"At some point, it is enough," Stephan Kramer, General Secretary of the Council, told Reuters.
He also complained that in previous years the Council's leaders, including Holocaust survivors, had been given seats among other visitors in the gallery rather than in the main plenary hall.
"This symbol speaks for itself and is unsurpassable in terms of its lack of respect," Kramer told Die Welt newspaper.
He criticized politicians for failing to adjust the protocol at a time when Germany was seeing a record number of far-right crimes and when Pope Benedict was rehabilitating a bishop who had denied the extent of the Holocaust.
In his speech, Koehler said Germans had a duty to protect Jews and the constant threat of anti-Semitic attacks was shameful in the country responsible for the Holocaust.
"It is a scandal that police have to protect Jewish places from old and new extremists," said Koehler. "Let us stand on the side of our fellow Jews. Whoever attacks them, attacks us all."
Nazis killed some six million Jews in the Holocaust. An increase in Germany's Jewish community in the last few years is mainly due to an influx from the former Soviet Union.
Violent right-wing crime, which includes anti-Semitic offences, jumped 9 percent in 2007 and the Interior Ministry has said it was up significantly in the first half of last year.
Synagogues and Jewish community centers usually have round-the-clock police guards and there are regular reports of vandalism of gravestones in Jewish cemeteries.
"We can't allow Holocaust deniers and extremists of any sort to find approval or understanding in our country," said Koehler.
"Whoever incites hatred against Jews and other minorities has learnt nothing from history," he added.
Pope Benedict has unleashed a storm of criticism from Jews by deciding to rehabilitate a British-born bishop who has denied the full extent of the Holocaust. Germany's Central Council of Jews has condemned the move.
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