His remarks followed a strongly worded statement from European Jewish and Muslim community leaders, which underlined that circumcision was fundamental to both faiths, and demanded that the German government intervene to grant the practice legal protection.
They described the Cologne court decision as: "an affront to our basic religious and human rights."
The statement was signed, among others, by the heads of the European Jewish Parliament, the Rabbinical Centre of Europe, the European Jewish Association, Germany's Islamic Union for religious Affairs and the Islamic Centre in Brussels. Leaders from both faiths also met members of the German and European parliaments to voice their anger at the court's decision and demand that clear legal protection of the rite be established.
Chancellor Merkel's government has so far avoided taking sides in the deepening debate in Germany.
However, the latest European Jewish and Muslim initiative will have dramatically increased the pressure on her coalition to take some action.
Germany's Green Party was among the first to respond yesterday. Renate Knast, the party's parliamentary leader said the Greens wanted to give Muslims and Jews legal security with new laws guaranteeing the right to circumcision on religious grounds. "We want to find a way which does not punish circumcision," she said.
In the wake of the Cologne court ruling Germany's Medical Association advised doctors to stop performing the operation because they could face legal consequences. The court's decision also prompted two Berlin hospitals to call a temporary halt to the procedure.
However, another influential doctor's organisation, the Hartmannbund said it fully supported Jewish and Muslim objections to the court's ruling. "Turning a hitherto generally accepted religious practice into a criminal offence amounts to one of the biggest forms of discrimination imaginable", said Bernd Lucke, a spokesman.
The Cologne ruling centred on the case of a four-year-old Muslim boy who was circumcised in one of the city's clinics in November 2010 on the express wishes of his parents.
Two days after the operation, the child's mother took the boy to the accident and emergency unit at Cologne University hospital because he was suffering from severe bleeding. State prosecutors subsequently charged the doctor who performed the operation.
A lower court found that the doctor had carried out the operation properly and ruled that the child's circumcision was in his interests as it signified his membership of the Muslim community. However the prosecution appealed to a higher Cologne court which overruled the lower court's verdict.