Congregations across the state of Iowa are in grave danger of having their pastors silenced in the pulpit over LGBT public accommodation rules, according to a federal lawsuit filed against the Iowa Civil Rights Commission.

Fort Des Moines Church of Christ filed what is known as a “pre-enforcement challenge” – arguing that a portion of the Iowa Civil Rights Act is a threat to First Amendment freedoms.

Click here to join Todd’s American Dispatch: a must-read for conservatives!

Alliance Defending Freedom, a legal firm that specializes in religious liberty lawsuits, is representing the church in its fight against the commission.

“Churches should be free to teach their religious beliefs and operate their houses of worship according to their faith without being threatened by the government,” ADF Legal Counsel Christiana Holcomb said. “That is a foundational First Amendment principle.”

The issue involves the commission’s interpretation of the 2007 Iowa Civil Rights Act – specifically about public accommodation.

The law includes a facility use mandate that requires anyone subject to the law to open sensitive areas to people based on their gender identity rather than their biological sex.

So does the law apply to churches? The commission answered that question in a brochure on the matter:

“Sometimes. Iowa law provides that these protections do not apply to religious institutions with respect to any religion-based qualifications when such qualifications are related to bona fide religious purpose. Where qualifications are not related to a bona fide religious purpose, churches are still subject to the law’s provisions. (e.g. a child care facility operated at a church or a church service open to the public.)”

ADF alleges that interpretation would allow the government to censor the church’s teachings on biblical sexuality and force them to open its restrooms and showers to members of the opposite sex.

So who gets to decide what is and is not a bona fide religious activity?

Kristina Johnson, the executive director of the commission, told me they would have to investigate each activity on a case by case basis.

“Some churches host outside activities like AA or Al Anon, with no connection to the church’s mission or doctrine,” she told me. “The statute requires the Commission to review whether the ‘qualifications are related to a bona fide religious purpose.”

So the government is going to dispatch agents to investigate the religious activities of Iowa churches – to determine if they are in fact religious?

Most churches would consider every activity to be connected to some sort of ministry – whether it’s a day care center or church pot-luck or sports programs like Upward Basketball or Upward Soccer.

Would churches that engage in those sorts of activities be required to comply with public accommodation laws?

“As a church, they can believe whatever they want,” Donna  Red Wing, the executive director of One Iowa, told the Des Moines Register. “They cannot, however, break the law when providing public accommodations.”

One Iowa is the state’s largest pro-LGBTQ rights organization.

Red Wing expounded on what constitutes a public accommodation in a separate interview with television station KCCI.

“That could be a camp open to all kids, could be a food pantry,” she said. “If they receive funds from local, state or federal government, that takes them out of the bona fide religious activity into public accommodation.”

Attorney Holcomb argued that every event held at a church on its property has a bona fide religious purpose and the commission has no right to violate First Amendment rights.

“Churches have always been protected from government intrusion, and they still are,” she said. “They have a firmly established freedom to teach their beliefs and set internal policies that reflect their biblical teachings about marriage and human sexuality.”

First Liberty Institute filed a separate complaint earlier this week on behalf of Cornerstone World Outreach, a church based in Sioux City.

Hiram Sasser, the law firm’s director of litigation, said the Commission’s brochure means churches would be required to let transgender individuals use the bathrooms of their choice.

“It further compels our client to use specific pronouns when referring to certain ‘gender identities’ and prohibits our client from even teaching its religious beliefs,” Sasser said.

“Cornerstone World Outreach cannot be made to open its restrooms for use by individuals in accordance with their gender identities, rather than their sex assigned at birth,” Sasser said.

Click here to get Todd’s best-selling book – an indepth primer on how to restore traditional American values!

Chelsey Youman, First Liberty’s chief of staff, told me the ramifications of Iowa’s policy cannot be overstated.

“This is an unprecedented move by a government agency to mandate that anytime a church opens its doors to the public that it automatically qualifies as a place of public accommodation,” Youman said. “And this is just the tip of the ice berg.”

Pastor Cary Gordon accused the Iowa Civil Rights Commission of “acting like a First Amendment Gestapo – to hunt down and harass churches and local businesses trying to live out their Christian convictions.”

“Based on what they are saying, orthodox Christianity is in violation of the state law of Iowa,” the pastor told me.

For the record, not a single church has been subjected to a complaint or investigation, the commission told me.

But I predict that it’s only a matter of time before a militant LGBT activist tries to target a congregation. It’s only a matter of time.

Todd Starnes is host of Fox News & Commentary, heard on hundreds of radio stations. His latest book is "God Less America: Real Stories From the Front Lines of the Attack on Traditional Values." Follow Todd on Twitter @ToddStarnes and find him on Facebook.