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Police are also trying to crack down on anti-Semitic chants by having translators accompany the Friday march and record any illegal utterances.
Jewish leaders condemned anti-Israel and anti-Jewish chants during protests in Germany last weekend against the U.S. decision to recognize Jerusalem as Israel's capital.
Berlin police said the marchers Friday were warned in Arabic and German about restrictions, including the ban on flags.
Police said the march will be filmed, adding: "we will not tolerate forbidden utterances."