Rt Revd Vitus Huonder, the Catholic bishop of Chur, quoted a passage from the Bible which said homosexuals should be punished by death at an event.
At the 'Joy in Faith' forum in the German city of Fulda, he quoted two verses from the book of Leviticus, including Leviticus 20:13.
He told the gathered: "Both of these passages alone suffice to clarify unambiguously the church's position on homosexuality".
The bishop has since released a statement saying it "wasn't my intention" to suggest gay people should be killed.
He said he regretted that his comments had been misunderstood.
Swiss gay rights organisation Pink Cross said it had made a criminal complaint about the comments.
It said it was "shocked and angry" by the comments and wanted a "public apology for the latest gaffe".
The bishop has previously provoked controversy when he called for a priest who had blessed a lesbian couple to be sacked.