"There must be no tolerance for attacks against synagogues in our country," Foreign Minister Heiko Maas told the Funke media group, pledging "unwavering security" for Jewish temples in Germany.
Protesters burned Israeli flags outside synagogues in Muenster and Bonn in western Germany earlier this week, with 16 people arrested.
On Wednesday evening, around 180 people shouted anti-Israeli slogans at a march in Gelsenkirchen also in the west.
Police said they prevented the protesters from marching on the city's synagogue.
In Hanover police said they broke up a protest of around 550 people and prevented two protesters from burning an Israeli flag.
Maas said German Jews should not be made scapegoats for the events in Israel "either in the street or on social media".
Germany's Central Council of Jews, which represents about 200,000 Jews living in the country, on Wednesday called for stepped up protection for Jewish institutions in the country as unrest flares between Israel and Palestinians.
READ ALSO: Germany's Jews call for protection amid Israel-Palestinian clashes
Dozens have been killed in days of violence -- mostly on the Palestinian side -- with both sides exchanging deadly fire in some of the worst unrest in years. Â
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