Homeless shelters have become the latest battleground in the national debate over transgender rights.

The Department of Housing and Urban Development (HUD) is expected in September to finalize regulations that would allow people to stay in homeless shelters based on the gender they identify with.

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The proposal has set off a firestorm, pitting LGBT groups against religious organizations that operate many homeless shelters.

“Transgender women are women regardless of whether they were born male,” said David Stacy, government affairs director at the Human Rights Campaign.

“If you’re a transgender woman and you walk into a homeless shelter and they treat you like a man, it’s traumatizing,” he added. “These people are already vulnerable, they’re homeless, they don’t have a job. To face discrimination the entire time they’re there is a real problem.”

Religious organizations see things differently.

Tim Wildmon, president of the conservative American Family Association, lamented having to “make room for people who are sexually confused at the expense of everyone else.”

“No one is in favor of beating up transgender people,” Wildmon told The Hill, “but why do you have to force other people to feel really uncomfortable, and in some cases unsafe, just to make your political point?”

“What if I self-identify as a woman today, and tomorrow I want to self-identify as a man?” he asked. “Why not self identify as a minority? Today, I’m white. Tomorrow, I’m black.”

The controversy comes on the heels of a contentious North Carolina law that requires people to use public bathrooms that match their assigned gender at birth. The Department of Justice has sued to stop the law, putting transgender issues at the forefront of the 2016 campaign.

HUD’s proposed regulation instructs homeless shelters to disregard the “complaints of other shelter residents” who feel uncomfortable living with someone who is transgender.

"It is likewise prohibited to deny appropriate placement based on a perceived threat to health or safety that can be mitigated some other less burdensome way,” the proposal says.

The agency declined to comment on the rule until after it is finalized.

According to a 2011 survey from the National Center for Transgender Equality, 29 percent of transgender people who sought emergency shelter had been rejected at some point in their lives, while another 42 percent were forced to stay in shelters for the gender they were assigned at birth.

The Center for American Progress and Equal Rights Center conducted a more recent 2016 study that found only 30 percent of homeless shelters in Virginia, Connecticut, Tennessee and Washington state accommodate transgender women.

The Fair Housing Act prohibits homeowners from refusing to sell or rent to people because of their race, religion or gender, but HUD is looking to extend similar protections to homeless shelters that provide short-term housing.

Congress has not passed discrimination protections for transgender people at homeless shelters, so the rules would only apply to those shelters that receive financial assistance from the federal government.

“It makes no sense at all,” Wildmon said. “Good, Christian organizations that are trying to help people do not need Washington dictating their bathroom or bedding policies."

Catholic Charities USA, which did not respond to requests for comment, and the Association of Gospel Rescue Missions both raised concerns about the transgender policy in comments filed with HUD.

Opponents of the regulation say homeless shelters should be a safe haven for women who have been abused by their husbands and boyfriends. They say those women may feel that they are in danger living with a transgender woman who was born a man.

LGBT advocates say those fears are overblown.

“We, obviously, need to protect women who have been sexually abused,” Stacy said. “But if we don’t treat people consistently with their gender identity, then a woman who was abused by her boyfriend could be housed with a transgender man who looks like a man and has a beard.”

LGBT advocates say they are more concerned about protecting transgender women who are vulnerable when being housed with homeless men.

The National Center for Transgender Equality survey found that 55 percent of transgender people who stayed in homeless shelters claim they were harassed by staff, while 1 in 4 say they were physically abused and 22 percent say they were sexually assaulted.

“If you view someone as less human, it’s easier to have a higher level of violence against them,” Stacy said.

Critics of the regulation have also raise the potential for men to pose as transgender women.

“One of the guests at a rescue mission overheard someone on the street saying, ‘Dude, if you go down to the rescue mission and tell them you’re transgender, you can sleep in the women’s dorm and even shower with them,’” said John Ashmen, president of the Association of Gospel Rescue Missions. “So that idea is out there, but I don’t know of any missions that have called the police because of it.”

“No one is trying to make transgender people feel awkward, but we’re concerned about the well-being and safety of everyone in our rescue missions,” Ashmen said.

HUD’s transgender policy would not provide a “get-out-of-jail-free card” for men who take advantage of the rules to prey on homeless women, Stacy said.

"Nothing in this proposed rule is meant to prevent necessary and appropriate steps to address any fraudulent attempts to access services or legitimate safety concerns that may arise in any shelter,” HUD wrote in its proposal.