At every city of Aiken meeting, a member takes a turn saying a prayer or blessing, but Cavanaugh opted for a minute of silence instead, in response to a challenge to the opening prayer.
The city administrator's office received an eight-page letter at the end of June from the Freedom From Religion Foundation, a nonprofit group based in Madison, Wis., that investigates what it terms violations of the separation of church and state.
Rebecca Markert, an attorney for the foundation, submitted the letter to city council on behalf of an Aiken resident. Markert said she couldn't comment on the resident's complaint specifically, but labeled the city's prayer unnecessary at a secular meeting.
"We'd prefer if they'd drop prayer altogether," she said.
Markert's staff compiled all the prayers from meetings in 2010 and said many of them are predominantly Christian.
"We understand that these prayers are almost always addressed to God, and end 'in Jesus' name' or some variation thereof, such as 'in your Son's name,' " the letter stated.
The group said council also violates Fourth Circuit ruling against government-sponsored prayers that are sectarian, denominational, and invoke a particular faith or deity.
The organization has more than 16,000 members, with more than 100 members in South Carolina, Markert said.
City Administrator Roger LeDuc said council members decided they would continue with prayer again at the next meeting in August, despite the complaint, because they feel it's something that's important.
"We just can't use what would be referenced to Christian faith," said LeDuc. For example, the prayer will reference God, but not Jesus.
LeDuc encouraged council members to write out a prayer if they felt they may fall into violation of the rule.
Now every Aiken County governing body is double-checking its compliance.
Aiken County Council and the school district have never received a complaint although they have prayed before meetings for more than 30 years.
Aiken County Council chairman Ronnie Young has said he will continue the practice as he and Councilman Willar Hightower have for years.
Aiken County Schools attorney Bill Burkhalter said although schools and sporting events are regulated by state laws invoking a moment of silence, the school board has an open-ended practice of prayer before meetings rather than a policy.
"They are adult board members and have a broader range of discretion," he said.
The prayers are alternated among district-level administrators and board members, and some have opted for inspirational poems in the past instead of a prayer.
Markert said for now the organization will deal with the complaint with the city first, but additional examination of other governing bodies may follow.
She declined to say what action the organization might take.