State prison officials were grappling Wednesday to establish a new policy for housing transgender inmates following a court order handing the Correction Department custody of a transgender minor.

The youth is a 16-year-old who is biologically male but has long identified as a female, according to a court document transferring the teen from the custody of the Children and Families Department to the DOC. The juvenile was committed to DCF in November after assaulting someone at Bridgeport Detention Center.

In the juvenile system, the teen has been recognized as a transgender female and has been housed in female living sections at child detention centers and DCF facilities, or in isolation at male facilities.

But the court ordered the youth transferred to the DOC, initially for an assessment at the state’s only women’s prison. Then the correction commissioner will decide where she will be placed for a longer period.

Historically, DOC policy has been to place transgender people with the inmate population they correspond with biologically.

The youth’s lawyer, Assistant Public Defender James Connolly, said the policy presents a civil rights issue for his client. He’s concerned the teen will be forced to look and behave like a male. That sometimes has severe psychological consequences for people who have what’s called gender dysphoria, or a disconnect with their biological gender, he said.

“The outcome is often depression all the way to suicidal behaviors,” he said. “So, in addition to being a juvenile in an adult correctional facility who’s not been convicted of any offense, you can imagine how this gender identity issue may affect her.”

However, Michael P. Lawlor, the governor’s advisor for criminal justice policy, said the DOC was re-examining its policy and considering best practices from around the country.

“I think the time has come in Connecticut and every state for people to adopt a clear policy on this,” he said. “Moving forward, you want to have a process by which you treat prisoners consistent with state laws and we have gender non-discrimination policies on the books here in Connecticut.”

In 2011, the legislature passed a bill making it illegal to discriminate against someone based on their gender identity and expression. Gov. Dannel P. Malloy signed it into law.

But Lawlor said the issue gets complicated in the prison system. Correction administrators need to have a way to verify an inmate as being legitimately transgender. Otherwise, inmates could claim to be transgender in order to be transferred.

However, Lawlor said inmates already are evaluated based on a number of classifications. He said gender identity should be one of those classifications.

In the meantime, the teen has been ordered to the women’s prison for 72 hours. In a written statement, DOC Commissioner James Dzurenda said the department was working to accommodate the youth.

“We will do everything in our power to provide a safe, secure and humane environment for this individual, as we would for any other person under our supervision,” he said.

But some lawmakers and the state child advocate question why the teen was ordered into the adult prison system rather than being held at a recently-opened locked facility for troubled girls in Middletown. The Children and Families Department received funding to open the new facility despite outcry from some child advocates who claimed it was unnecessary.

State Child Advocate Sarah Healy Eagan has been working to keep the youth in juvenile programing rather than in an adult facility. Although Eagan said she’s confident that the DOC will do what it can to keep the teen safe, she said the state’s prison department has no precedent for how to handle the situation and no programming to offer.

“There’s not a blueprint for this,” she said.

Sen. Beth Bye, co-chairwoman of the Appropriations Committee, said she was “perplexed” as to why DCF would argue in court to have the youth turned over to an adult prison when its Middletown facility, called Solnit, is now open.

“I don’t understand why, now that Solnit is up and running — as I understand there are only four women there — why they wouldn’t put this woman [there]. That was the whole point. And now we have a case and there is a young woman in jail,” she said.

Although she questioned why the Middletown facility was not being used, Bye said she understood that the youth was difficult for the department to manage.

“There’s no doubt it’s a kid that’s very tough to deal with. Clearly,” she said.

In a written statement, the Children and Families Commissioner Joette Katz pointed to a rarely used law allowing a court to transfer a dangerous minor into an adult prison.

“The Department does not take such a step lightly. In fact, the only time the law was used to effect a transfer was more than 13 years ago. We work hard to serve youths with even the most complex needs, but in extreme cases, when a youth has seriously injured staff or assaulted other youths whom the department is entrusted to keep safe, thereby eroding the capacity of the impacted programs to serve, it is incumbent upon us to take appropriate authorized measures,” she said.