The Danville City Commission received a complaint from a national atheist and agnostic group.
The Freedom From Religion Foundation wrote a letter asking the Board of Commissioners to stop saying a prayer before its meetings.
Danville's Mayor says the meetings have started with a prayer for as long as he can remember.
Both sides claim their constitutional rights.
"When you go down the path of mixing religion in with the government, you get situations like you have in Afghanistan and Pakistan," said one of the complainants.
"It's freedom from religion. It's not freedom from religion," said Danville Mayor Bernie Hunstad.
One side is much larger than the other.
"In Danville, Kentucky we're an even bigger minority," said the complainant.
We spoke to two of the people who complained, both atheists. One did not want us to show his face, or use his name.
"Quite frankly I fear the backlash of any repercussions against myself, or my family in the area from the Christians," said the man.
"I get the perception, or the idea that they are really trying to impose their belief system," said Mayor Hunstad.
Ricky Smith contacted the Freedom From Religion Foundation. In December, he made a similar complaint against the Boyle County Fiscal Court. He declined to speak with us then. He says that experience encouraged him to speak out.
"I had a lot of supporters, lot of supporters I wasn't expecting. I'd like to have a moment of silence where everybody can pray to the god they want to pray to, or be excused from not having to sit through a religious ceremony," said Smith.
Mayor Hunstad questions Smith's motives.
"I actually don't believe that he's offended. I think that's his way of expressing opposition," said Hunstad.
The mayor says when it comes to this issue, there is no such thing as sitting on the sidelines.