The Los-Angeles-based Jewish group called on German lawmakers to provide legal safety for the practice, saying it would be "a stain on today's Germany" to let the court ruling stand.
Criminalising circumcision was “an attack on one of the fundamental principles of Judaism," wrote Rabbis Marvin Hier and Abraham Cooper, founder and dean and associate dean of the Centre in a letter to Merkel.
"For 3,500 years, every male child has entered the Jewish people through the rite of circumcision. We are not talking about a mere custom, but a biblical principle that has defined the Jewish people from time immemorial."
They noted that Nazi dictator Adolf Hitler said "in one of his infamous anti-Semitic rants" that "conscience is a Jewish invention, it is a blemish like circumcision."
"Since the defeat of Nazism, Germany has come a long way, and worked very hard to successfully chart a new course after the horrific legacy of the Holocaust by guaranteeing religious freedom and democracy," they wrote.
In a decision that sparked outrage from German Jewish and Muslim groups, a Cologne court last month ruled - in what could set a legal precedent - that the "fundamental right of the child to bodily integrity outweighed the fundamental rights of the parents."
The ruling marked a "big blow against integration," a spokesman for the Coordinating Council of Muslims in Germany, one of some 20 groups representing most of Germany's around four million Muslims, said on Wednesday.
German Muslim leaders urged lawmakers Wednesday to pass legislation protecting the right to circumcise boys after a court ruling against the practice when carried out on religious grounds.
Around 20 organisations representing most of Germany's around four million Muslims said parliament must ensure religious freedom by eliminating the legal uncertainty that now surrounds the practice.
"We call on the German Bundestag (lower house) and the government to act as quickly as possible to put an end to this legal insecurity and establish legal safeguards allowing the circumcision of boys," said Gurcan Mert of the Turkish Islamic Union, speaking on behalf of the other groups.
The ruling marked a "big blow against integration", Ali Kizilkaya, spokesman for the Coordinating Council of Muslims in Germany, another of the groups issuing the appeal, told the same news conference.
"Germany is a state based on the rule of law where rights, in particular religious liberties, are very important and I think that a ban (on circumcision) would not be good for Germany or Germany's image and concept of rights," he said.
"I hope this will be corrected quickly."
The Muslim groups are in contact with Jewish and Christian leaders on the issue and discussing how to bring pressure to bear on the political class, Ramazan Kuruguz from the conference of regional Islamic organisations said.
"We will speak with politicians and if necessary, we will of course hold protests and demonstrations," he said.
Thousands of young boys are circumcised every year in Germany, especially in the country's large Jewish and Muslim communities.
After the ruling touched off a storm of international protest, Foreign Minister Guido Westerwelle insisted the country would continue to protect religious freedom and rites including circumcision.
However several doctors and hospitals have said they would suspend the practice as long as its legal standing is unclear.