Huondor, known for championing ultra-conservative positions, sparked a storm of controversy while speaking at a July 31st debate on marriage and family organized by the German Catholic Forum in Fulda, Germany.
According to Swiss news reports, he cited a passage from the Old Testament that says men engaging in homosexual acts “are to be put to death; their blood will be on their heads”.
In a press release issued on Sunday, Pink Cross alleged that Huondor was indirectly “inciting people to crimes” with his remarks.
The umbrella organization said its complaint, to be filed on Monday, was backed by the Lesbian Organization Switzerland (LOS).
Pink Cross said that it highly values freedom of religion and expression but not when it results in people and organizations advocating “hatred and violence”.
Huondor later stated that he regretted having been "misunderstood", adding that he was misinterpreted as being contemptuous of homosexuals, the ATS news service reported.
“This was not my intention,” the bishop from the canton of Graubünden said in a statement.
But Bastian Baumann, director of Pink Cross, rejected Huondor's apology, noting that he had previously made anti-gay statements last year and in 2012.
“The bishop and his partisans preach hatred and afterwards always say they have been misunderstood.”