"I feel the decision is discriminatory and counters efforts to promote integration," said Ali Demir, the chairman of the Islamic Religious Community.
"This legal ruling is an outrageous and insensitive act," said Central Council of Jews in Germany President Dieter Graumann in a statement.
The Jewish council called the ruling an “unprecedented and dramatic infringement of the rights of self determination for religious communities.”
The District Court in Cologne ruled on Monday that non-medical circumcision was a "serious and irreversible interference in the integrity of the human body.”
The ruling was made on an appeal by the prosecutor of a case involving a Muslim doctor who performed a circumcision on a four-year-old boy.
The court's logic was that the young child's right to physical integrity had primacy over those of his parents to practice their religion.
Both Graumann and Demir rejected that, saying the ruling was a discriminatory and unfair intrusion into their religious freedom.
"This is a harmless procedure that has thousands of years of tradition and a high symbolic value," Demir said in a statement.
He also argued that there were advantages of circumcision in reducing the transfer of diseases. He said forbidding the practice would do nothing to stop it.
"We'll end up with circumcision tourism in neighbouring countries," he said.
Echoing his Muslim colleague, Graumann said: "Circumcision of newborn boys is an integral part of the Jewish religion and has been practiced worldwide for thousands of years. This religious right is respected in every country of the world."
Jewish boys are typically circumcised when they are eight days old, providing the child is healthy. Muslim boys are usually circumcised much later.
Graumann called on the German parliament to create a legal framework to ensure freedom of religious practice.