A spokesman for Chancellor Angela Merkel said government officials would work quickly to protect the practice of circumcision.
The Cologne court case last month involved a 4-year-old boy who suffered medical complications after being circumcised, the BBC reported. The judge in the case ruled a child's right to physical integrity trumps religious and parental rights.
Although the doctor involved in the case was acquitted, Germany's Medical Association advised doctors not to perform circumcisions after the ruling.
In a joint statement signed by leaders of groups including the Rabbinical Center of Europe, the European Jewish Parliament, the European Jewish Association, Germany's Turkish-Islamic Union for Religious Affairs and the Islamic Centre Brussels, Jewish and Muslim leaders said they considered the ruling to be "an affront [to] our basic religious and human rights."
Chancellor Angela Merkel's spokesman, Steffen Seibert, said it was a case of protecting religious freedom.
"For everyone in the government it is absolutely clear that we want to have Jewish and Muslim religious life in Germany. … It is clear this cannot be put on the back burner. Freedom to practice religion is a cherished legal principle," Seibert said, adding, "Circumcision carried out in a responsible manner must be possible without punishment."
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