Lancaster Mayor R. Rex Parris reportedly made the comments during his state of the city address.
The Council of American-Islamic Relations says Parris violated the civil rights of non-Christians last week and should not use his official role at a city event to advance a specific religion.
The civil rights group says Parris also talked about an April ballot measure that would endorse prayer at city meetings without restricting its content, including references to Jesus Christ.
The council of American-Islamic Realtions sent a complaint to the Department of Justice, requesting an investigation.
Meantime, Parris, who was elected in 2008, has refused to apologize.
The latest incident follows another incident involving remarks posted by a city councilwoman on her Facebook page.
Muslim community leaders criticized Lancaster Councilwoman Sherry Marquez for a posting about a Muslim New York man who is being tried for beheading his wife in 2008, days after she filed for divorce.
Marquez's posting included the comment, "this is what the Muslim religion is all about."
Marquez told the city council she was horrified by the killing and apologized for her comment.