"We have a new phenomenon, as we have many refugees among whom there are, for example, people of Arab origin who bring another form of anti-Semitism into the country," Merkel told the private Channel 10 network.
Her remarks come after an alleged anti-Semitic attack Tuesday in Berlin caused a stir in Germany.
According the German tabloid Bild, the main alleged perpetrator, who surrendered to police, is a Syrian refugee who lived in a centre for migrants near Berlin.
In the interview, Merkel said the German government had appointed a commissioner to fight against anti-Semitism.
"The fact that no nursery, no school, no synagogue can be left without police protection dismays us," she said.
Merkel also reaffirmed that Israel's security was a central concern for Germany because of its "eternal responsibility" for the Holocaust.
But she rejected the possibility that Berlin would follow Washington's example and move its embassy from Tel Aviv to Jerusalem.
"We must work for a two-state solution, and according to that, the status of Jerusalem must be clarified," she said.
The US move has angered Palestinians who see east Jerusalem, annexed by Israel, as the capital of any future Palestinian state.
Merkel also reiterated Germany's support for the continuation of the Iran nuclear deal, which provides for curbs to Tehran's nuclear programme in exchange for relief from international sanctions.
"We think it's better to have an agreement, even if it's not perfect, than no agreement," she said.
Israeli leaders and US President Donald Trump's administration think the deal – signed in 2015 between Iran and the world's five nuclear powers, plus Germany — is too lax.
Trump has threatened to restore sanctions against Iran and withdraw from the deal if his European partners do not "fix" it by May 12th.