Government spokesman Steffen Seibert told reporters that although Berlin opposed the move by US President Donald Trump last week, it strongly condemned protests in German cities where "hatred" of Israel and Jews was expressed.
"At certain rallies over the weekend, slogans were chanted, Israeli flags were burned and slander against the state of Israel and Jews in general were spread which were shameful," Seibert said.
"One has to be ashamed when hatred of Jews is put on display so openly on the streets of German cities."
He said that while Germany protected a constitutional right to free speech and assembly, that freedom did not cover incitement of racial hatred or violence.
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"It is important that we continue to stand up to all of that," he said.
German cities including Berlin and Munich saw anti-Israel demonstrations over the weekend.
At a protest late Friday in front of the US embassy in the German capital and again yesterday in the ethnically diverse Neukoelln district of Berlin, demonstrators burned the Israeli flag.