According to police statistics, at least 1,421 anti-Semitic crimes were committed in Germany last year.
"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 Israel’s private Channel 10 television broadcaster on Sunday.
"But unfortunately, anti-Semitism existed before this," she added.
Her remarks come after two men wearing kippahs were attacked in Berlin last week causing a stir in Germany, Euronews reported.
The newspaper Bild has reported that the alleged attacker, who turned himself in to police last Friday, is a Syrian refugee who lived in a refugee center outside Berlin.
Angela Merkel said the authorities had appointed a new commissioner to fight anti-Semitism.
She vowed to do everything possible to ensure the safety of Jews in Germany and reaffirmed that the security of the Jewish state remained a central concern for Germany because of its "eternal responsibility" for the Holocaust.
Angela Merkel has still agreed to take in an additional 10,000 migrants selected by the United Nations’ refugee agency (UNHCR).
During a meeting with the UN’s High Commissioner for Refugees, Filippo Grandi on Monday, Merkel said the refugees would be part of a resettlement program in Germany.
She didn’t mention the countries the refugees will come from.
Many in Germany are critical of Angela Merkel’s decision to open the country’s borders up to migrants from North Africa and the Middle East.
In 2015 alone, around one million arrived in Germany, sometimes at a rate of more than 10,000 people per day.