During the week of the inauguration of a president whose policies will lead to a sharp increase in migrant arrests, America’s newest immigrant detention centre opened in rural north Texas.

Known as Prairieland, it has an unusual feature designed to protect an especially vulnerable section of the population: a unit for transgender detainees. Some LGBT advocates, though, question whether holding transgender people in a detached pod in a remote location will do more harm than good.

The privately run centre 40 miles from Dallas stands as a monument to the Obama administration’s commitment to migrant detention, a practice it reinforced from 2014 as the southern border saw a surge in crossings by families and unaccompanied minors seeking to escape danger in troubled central American nations.

In fiscal year 2014, government figures show, Immigrations and Customs Enforcement (ICE) took 425,728 non-citizens into custody, up from about 85,000 almost two decades earlier.

Amid longstanding concern from human rights groups about the practice and the conditions inside the facilities – exacerbated by worries that the new administration will not be sympathetic to LGBT people – attention has increased on the treatment of transgender inmates. Human Rights Watch last year published a 68-page report detailing instances of abuse suffered by transgender women, many held in men’s facilities and in solitary confinement, already traumatised by abuse in their home countries that prompted them to seek safety in the US.

Many of these detainees have fled to the US precisely because of their gender identity, only to find themselves in places where their risk of being sexually abused is significantly higher compared to cisgender heterosexual, gay, lesbian or bisexual detainees, according to the Human Rights Watch report.

In 2015, ICE issued guidance aimed at improving conditions for transgender people, including taking into account their individual needs during detention, such as preferences about housing.

Prairieland is the second facility in the country with a specialised transgender unit. Out of 612 beds, 36 are designated for transgender people. The only other ICE facility that houses transgender immigrants in separate dormitories is in the Los Angeles area, in space rented in the Santa Ana city jail. It is reportedly ending its deal with ICE in 2020.

ICE said last week there were 55 self-identified transgender people in detention across the country, representing about 0.13% of all detainees; none were yet in Prairieland.

“ICE is committed to providing a respectful, safe and secure environment for all its detainees, including transgender individuals. Discrimination or harassment of any kind based on a detainee’s actual or perceived sexual orientation or gender identity is strictly prohibited. The transgender dorm at the Prairieland Detention Center is designed to help minimize conflict,” an ICE spokesman said by email.

The newest immigration detention center has a separate unit for transgender inmates. Photograph: Charles Reed/US Immigration and Customs Enforcement

The hope is that future detainees will not suffer the kind of experience endured by Ishalaa Ortega. A transgender woman now applying for a green card, she was detained in California about five years ago after arriving from Mexico where she feared for her safety because of her political activism.

Ortega said that after several days in a cramped and unpleasant holding facility, she was taken to a centre in San Diego and asked if she was afraid to be placed with men in the general population.

“I said, ‘Of course I am, I don’t want to be there,’” she recalled. “What they said is, ‘You don’t want to say that because you will be placed in solitary confinement.’ That was my choice, being with males or being in solitary confinement.”

Ortega opted to be placed with the male population, where there were five transgender people and a few gay men. She stayed for nearly two months. “I did not suffer any violence. I’m a very tough person, I’m tall,” she said. “The other ones were suffering from a lot of comments, a lot of judgment.” She added that at first the guards did not read the notes on her intake form, so she was not afforded the extra security of a cell covered by a camera.

Some advocates do not believe an at-risk section of the population should be detained at all while their cases are processed and doubt if staff will truly be able to guarantee their safety and wellbeing.

“This detention centre’s got all of the bells and whistles, all of the latest technology,” said Andrea Aguilar, who has toured Prairieland. She is the managing attorney for the Dallas-Fort Worth offices of Raices, which provides legal services to immigrants. “No matter how nice a detention centre is, our position is that the government shouldn’t be detaining immigrants because it’s a civil procedure.”

Aguilar worries about whether placing transgender people apart from the general population could stigmatise them, even if it seems to offer safeguards in principle – and whether healthcare will be adequate.

Despite the growing use of video-conferencing, Aguilar said that “a lot of times it’s just hard to access the detainees despite all the technology that’s available”.

Logistical and bureaucratic issues can result in attorneys waiting for hours to speak with clients, she said – and whether an immigrant has legal representation has a profound impact on a case’s prospects.

Being transferred to Prairieland from elsewhere in the country may make it harder to connect transgender individuals with legal help, among other concerns, said Aaron Morris, executive director of Immigration Equality, an LGBTQ immigrant rights group. “There is a danger that using this as a safety mechanism will also seem quite punitive to people, as they will not self-identify,” he said.

“We have some women in New Jersey who have declined being transferred to Santa Ana and their only other option if they want to stay near their lawyer, near their communities, near their families, near their children, is to stay in a men’s facility and for a trans woman, that is not much of an option.“

It would be far better, he argues, to use other methods such as release on recognisance, placing immigrants in the care of community organisations, ordering regular check-ins with ICE or employing electronic monitoring devices like GPS ankle bracelets. “The alternatives to detention are so much more humane, so much more cost-effective,” he said.