“They are all greatly concerned about the ramifications of the ruling, but mostly for Jewish and Muslim life in Germany,” Mr. Westerwelle said. There are 100,000 Jews and four million Muslims living here.

When the time came to have their son circumcised at age 4, Muhsin Sapci and his wife, Gonca, both first generation immigrants from Turkey, assumed they would simply take the boy to the nearby Jewish Hospital, used by many Muslim families who also prefer to have the procedure done by a surgeon.

But since a German court’s ruling that equated circumcision with bodily harm — and a criminal act — many hospitals across the nation have stopped performing the procedure. The Sapcis are determined to have their son, Asil, who turns 4 this month, circumcised, but they do not know where to go.

“Right now everything is controlled, most people go to a doctor and the child is covered by insurance,” Mr. Sapci said. “If they try to outlaw it, it will still be done, but differently, and that could have consequences.”

Their quandary is indicative of the confusion that has been sown by the ruling on June 26 by a court in Cologne that, while not enforceable outside that region, has sent ripples of anger and anxiety throughout the country and beyond. It has raised vexing questions about the boundaries of religious practice and freedom in an increasingly secular Germany.

“The often very aggressive prejudice against religion as backward, irrational and opposed to science is increasingly defining popular opinion,” said Michael Bongardt, a professor of ethics from Berlin’s Free University who added that the ruling reflected a profound lack of understanding in modern Germany for religious belief.

Jewish and Muslim organizations convened this week in Berlin and Brussels to protest the ruling vigorously, and they said they had been inundated with calls from confused parents. The German Medical Association condemned the ruling for potentially putting children at risk by taking the procedure out of the hands of doctors, but it also warned surgeons not to perform circumcisions for religious reasons until legal clarity was established.

On Friday, as the outcry intensified, the issue reached the highest levels of the German government. Chancellor Angela Merkel’s spokesman said that discussions were under way between the chancellor’s aides and the justice and other ministries to find a legal solution that would protect the right to perform ritual circumcisions.

“It is urgently necessary that we establish legal certainty,” said the spokesman, Steffen Seibert. “It is clear this cannot be put on the back burner. Freedom to practice religion is a cherished legal principle.”

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