German police attribute more than 90% of cases nationwide to far-right offenders. But Jewish activists and victim representatives say the data is misleading because police automatically label any incident where the perpetrators aren’t known as coming from the far right.

The problem goes beyond Germany. The recent murder of an elderly Holocaust survivor in Paris earlier this month in what prosecutors said was an anti-Semitic attack has fueled a perception that anti-Jewish acts—from casual insults to brutal violence—are on the rise across Europe and that governments appear unable to do much about it.

Levi Salomon, head of the Jewish Forum for Democracy against Anti-Semitism, a Berlin-based organization that documents hate crimes against Jews, says most violent incidents these days come from Muslim perpetrators.

“It is wrong to generalize or to stigmatize Muslim communities,” Mr. Salomon said. ”But to say there is no specific problem there is even worse. We need to devise urgent strategies to deal with this.”

Others paint a more nuanced picture, saying prejudice and stereotypes harbored by recent migrants from largely Muslim countries have added to an existing undercurrent of anti-Semitism among some Germans and older migrant communities from Eastern Europe, resulting in an increasingly threatening environment.

Liam Rückert, a 15-year-old Jewish student in Berlin, said he was recently mobbed by Arab and Polish classmates. And Klara Kohn, a 16-year-old whose father survived the Auschwitz death camp and Dachau concentration camp, said German students at her elite school in Hanover had taunted her, chanting “gas for the Jews!”

Heinz-Peter Meidinger, head of Germany’s teachers association, said a particular hot spot of anti-Semitism seemed to be schools, many of them in Berlin, where children from migrant families made up between 70% and 100% of students.

“The key part of the problem are the parents,” Mr. Meidinger said. “But we can’t reach them as teachers. Most of them don’t speak German and they are sometimes hostile toward authorities.” He said there was a tendency among Arabic- and Turkish-speaking communities to view Jews in Germany in the context of the Israeli-Palestinian conflict.

The very word “Jew,” Mr. Meidinger said, is now a generic term of abuse in some school yards.

In an interview at this family’s home this week, Solomon Michalski said his tormentors were “actually cool kids, but they get this from their parents.”

Solomon—the boy’s middle name, which he asked The Wall Street Journal to use—changed schools after he was threatened, but he found himself revisiting his ordeal last week after reports that a 7-year-old Jewish girl had faced similar threats at another Berlin school.

Solomon’s parents, who until recently hosted a Syrian refugee, took no action until their son came home with bruises. After that, Wenzel Michalski, Solomon’s father and head of the German branch of Human Rights Watch, invited his parents, Holocaust survivors, to hold a lecture at the school.

That changed little. A teacher said Solomon should try to avoid provoking the Palestinian student who was his most violent tormentor, Mr. Michalski says. The school management later apologized in a statement, pledged to investigate the anti-Semitism allegations and to ensure the perpetrators faced consequences.

Teachers have also faced abuse from their own students. Jessica Schmidt-Weil, who taught a class of teenagers of predominantly Middle Eastern origin in Berlin, said she changed schools two years ago after being abused by students. She now keeps her Jewish faith a secret.

The notion that some among the well over a million recent arrivals—many from Syria, where criticism of Israel laced with anti-Semitic clichés has been part of the official discourse for decades—might be harboring prejudice about Jews has presented authorities here with a dilemma.

Jewish representatives say Germany’s tried and tested tool set to combat anti-Semitism through education is failing to reach communities that often don’t speak German and know little about Nazism and the Holocaust.

Barbara John, a former Berlin integration czar, said cases of Arab families resisting Holocaust education or refusing to send their children on the traditional school trip to concentration camps have come up since the 1960s.

Back then, however, Germany’s Jewish community, half-a-million strong before Hitler’s rise to power, had become virtually extinct. It began growing again in the 1990s thanks to immigration from the former Soviet Union and, more recently, from Israel, making the fight against anti-Semitic prejudice an even more urgent necessity. Germany now has an estimated 200,000 Jews, more than 100,000 of whom are in Berlin.

Persistent complaints about the quality of crime statistics prompted Berlin authorities to team up with Jewish organizations in 2015 and set up Rias, an independent institution that collects data about anti-Jewish incidents, from hate speech to assault.

Benjamin Steinitz, head of Rias, counted 936 such incidents in Berlin in 2017. The police registered only 288.

This year, the newly appointed government of Chancellor Angela Merkel announced it would create the country’s first commissioner for combating anti-Semitism, now expected to be named in April.

With the media now increasingly pointing the finger at Muslim perpetrators, some Islamic organizations are taking steps to combat prejudice among their members.

Aiman A. Mazyek, president of the Central Council of Muslims, said it would make 10 imams available to join with rabbis and visit problematic Berlin schools.

“There is racism attached to every religion,” Mr. Mazyek said. “Our job is to help remove racism from our midst and educate people about our religion, to explain that we are devoted to living in respect, peace and tolerance with other religions.”

As for Mr. Michalski, he says he recently started googling property prices in Israel. “For the first time I’ve seriously thought about leaving. I hope it won’t come to that,” he said.

—Ayla Albayrak in Berlin contributed to this article.

Corrections & Amplifications 
The American Jewish Committee was incorrectly referred to as the American Jewish Congress in an earlier version of this article. (April 3, 2018)