"Singing can cause an increased release of potentially infectious droplets, which can also be spread over longer distances."
Protestant leaders have agreed to a temporary ban, but Catholics are unhappy.
"If the social distancing rules are observed, there is no reason to do without singing," a position paper prepared by the Catholic Bishops' Conference said.
"We see quiet singing and praying as possible," Matthias Kopp, a spokesman for the Bishops' Conference, told Bild newspaper.
And while their Protestant church leaders have agreed to the ban, many are less supportive.
"Every child knows singing together promotes wellbeing, strengthens the psyche, creates a bond between generations and is good for the soul," said Peter Hahne, a leading Protestant theologian.
Christian hymns are not the only religious celebration in the regulators' sights.
The Jewish community has reportedly agreed to dispense with the ritual of kissing the Torah.