Earlier this month, a lower court banned the practice on the grounds it causes bodily harm to babies, sparking anger among Muslim and Jewish citizens who cited their religious freedom.
The government has pledged to find a way around the ban "as a matter of urgency," but people such as Mimi Lipsis and her husband, Leo, remain concerned about the situation.
Their young boys have been circumcised in keeping with their Jewish faith, but if she gives birth to another, she might not be able to have him circumcised in Germany.
The controversy stems from a recent decision in a regional court in Cologne that made the circumcision of boys a criminal act, saying it causes bodily harm. The ruling, which does not apply on a national level, has left the Jewish community shocked and outraged.
"I don't think there's any bodily harm," Mimi Lipsis told CBC News. "I think in Judaism, when the child is seven days old, it's not a physical harm.… It puts a very sad light on Germans and on Germany."
The decision in Cologne to criminalize circumcision — in which the foreskin of the penis is removed with a scalpel — was finalized after a doctor carried out the procedure on a four-year-old Muslim boy in a way that led to medical complications, prompting an investigation and charges against the doctor. He was acquitted.
Martin Boese, a University of Bonn law professor, said the court based its decision on whether the need for the procedure justifies the surgery.
"The difference between circumcision and surgery is that there is a reason to do a surgery — it's for the health of the child," Boese said. "In this case, the court says religious reasons are not enough to justify this kind of surgery."
Boese said the ruling also raised questions about the religious rights of the child. "I think this is the first case where this question comes up: Are the parents entitled to give their consent or not?"
In their ruling, the Cologne judges concluded circumcision went "against the interests of a child to decide later for himself what religion he wishes to belong to."
Serdar Yazar, a spokesman with an organization that represents Turkish migrants in Germany, said the ruling is a slap in the face for Muslims.
"The perception is that it's a kind of Islamophobia," he said, "and it's a sign Islam is not part of Germany — that Muslims don't belong to German society."
For the Lipsis family, the issue transcends both religions.
"Germany can't afford this level of Islamophobia, either," Mimi Lipsis said. "It's not about Judaism or about Islam in particular. It's about religious freedom in a broader sense."
Since the ruling, the Jewish Hospital in Berlin has stopped all ritual circumcisions.
A surgeon at the hospital told CBC News he has had to cancel five circumcisions since the ruling in Cologne, for fear that he would face a similar charge.
"On one hand, you have freedom of religion and parental rights. On the other, you have criminal law that says you can only perform this procedure if it's for the well-being of the child," Martin Mueller said. "But the question is, what is actually good for the child: preventing bodily harm or providing religious freedom?"