A small Kansas town that has found a creative way to tap the pockets of taxpayers and businesses for road improvements is being sued by two local churches who argue that the city is taxing church attendance.

The Alliance Defense Fund filed a lawsuit this week on behalf of a Baptist and a Catholic church in the small town of Mission for charging them along with the rest of the city's property owners a transportation utility fee that has been dubbed derisively by critics as the "driveway tax."

City officials estimate that the fee, which is based on the size of the properties and the amount of traffic they generate, will raise $750,000 a year to help fund a $38 million project to fix the town's deteriorating roads.

Single residences in Mission, which has a population of 10,000 that rises to as many as 50,000 in the daytime, pay a flat fee of $72 per year but some businesses, like Target, pay as much as $46,000 annually, Mayor Laura McConwell told FoxNews.com.

"We thought it was a fair way to contribute that wouldn't put an unfair burden on any one group in our community," she said.

But the First Baptist Church of Mission, which has several dozen off-street parking spaces around the property and was charged nearly $1,000, and St. Pius X Catholic Church, which has three driveways leading to parking for nearly 250 vehicles and paid $1,700, say they shouldn't have to bear that cross.

"It's pretty clear that the city of Mission is taxing church attendance and that's not something they should be doing," Erik Stanley, senior legal counsel with the Alliance Defense Fund, told FoxNews.com. "They don't have the power do it. We're confident once we get to court, the judge is going to agree."

Stanley argues that the fee is actually a property tax, which he says churches, charities and other nonprofits have been exempt from paying.

"Mission does not have the power to override the property tax exemption granted by the state legislature," he said.

McConwell and other city officials declined to discuss the lawsuit, saying they had been advised by counsel to remain silent.

But McConwell said that city officials took several years and used a public process to find a way to finance fixing deteriorating roads that residents and businesses have long complained about. Charging property owners surrounding the road projects "would be cost prohibitive to residents and small businesses," she said.

City officials liked the transportation utility fee because it was "user-based" and "not tied to property taxes."

McConwell disputed the notion that the fee had anything to do with driveways. Instead, she said, it is based on the use of the property and the size of the building.

Similar fees were struck down by the state Supreme Courts in Idaho and Florida, who ruled they were taxes. Cities in those states are unable to pass any new property taxes unless the statehouses empower them to do so.

In Kansas, local governments can levy their own taxes as long as they don't conflict with state laws. Stanley says he believes a court will exempt all nonprofits, including churches, from the ordinance.

Stanley defended exempting churches from paying their fair share to improve the roads, saying churches in Kansas have always been exempt from property taxes and should remain exempt.

"There's two reasons they're granted exemption," he said. "They provide great social services to the poor and disadvantaged. They relieve that burden off of the government."

"The other reason is tangible benefits. Churches are active in forming good citizen. That is a tangible that the government benefits from. It goes back to every dollar the government takes from the church is putting those burdens back onto the government to take care of. So it doesn't make any sense to tax churches."