The U.S. military has a manual for everything, from how to dress to how to wage war.

Now the Pentagon has sent out a detailed written instruction to commanders on how a service member can change his or her sex in a step-by-step process that allows for extended time off.

The directive restricts personnel from living their “preferred gender” lifestyle, or “Real Life Experience,” on a military base among peers until the sex change transition is complete.

The Army, Air Force, Marine Corps and Navy must set up a bureaucracy — dubbed the Service Central Coordination Cell — to guide commanders overseeing sex change transitions.

A service member’s commander plays a big role in shepherding the patient through the sex transition. This starts with approving government-funded medical treatment of genital reconstruction surgery and hormone therapy, and then recovery, and then the final phase of determining the member’s fitness to return to duty after he or she receives a new official “gender marker.”

Commanders must hold training sessions to indoctrinate troops on transgender issues and nondiscrimination.

In announcing his intention to remove the ban on transgender personnel, Defense Secretary Ashton Carter last year said the rules were “outdated and are causing uncertainty that distracts commanders from our core missions.”

“We have transgender soldiers, sailors, airmen and Marines — real, patriotic Americans — who I know are being hurt by an outdated, confusing, inconsistent approach that’s contrary to our value of service and individual merit,” Mr. Carter said.

A Rand Corp. study estimates that the active force of 1.3 million has 1,300 to 6,600 transgender service members.

Robert Maginnis, a retired Army officer who has opposed President Obama’s policy of gays in the military and women in land combat, said Mr. Carter is “delusional if he believes our military needs transgenders/transsexuals to remain the ‘finest fighting force in the world.’”

“Transsexuals suffer from more psychiatric pathologies than the general population, and active suicide ideation and major depression episodes occur more frequently within this group,” Mr. Maginnis said. “Creating a bureaucracy to sort out transgender issues will go down in the history of our armed forces as the worst waste of defense dollars ever.

“Further, hiring a medical staff to provide ongoing treatment for these people robs precious money better used for treating our war wounded,” he said.

Taking effect Oct. 1, the elaborate 18-page instruction requires that a service member obtain a physician’s diagnosis that becoming a transgender person is “medically necessary” for the man or woman to meet military obligations.

Commanders must be bias-free, the directive says. They are given the option of putting a transgender individual on extended leave depending on how long the sex change takes.

If a transgender combatant is not deployable, the person must be judged in the same way as personnel with other medical conditions.

“Commanders will assess expected impacts on mission and readiness after consideration of the advice of military medical providers and will address such impacts in accordance with this issuance,” the document says.

Personnel will not be able to live as their “preferred gender” in the pre-transition phase called “Real Life Experience (RLE),” the instruction says.

“Although in civilian life this phase is generally categorized by living and working full-time in the preferred gender, consistent application of military standards will normally require that RLE occur in an off-duty status and away from the service member’s place of duty, prior to the change of a gender marker,” the document says.

A “preferred gender” status person must notify his or her commander of a diagnosis that gender transfer is a medical necessity, the treatment that is needed and the estimated date for a new gender marker. Even after achieving the marker, he or she may continue to require military medical treatment.

Once the transition is complete, transgender personnel must use the berthing, showers and bathrooms associated with their new gender markers.

The Service Central Coordination Cell, or SCCC, will include medical, legal and personnel management workers to give “expert advice and assistance to commanders with regard to service by transgender service members.”

“Where possible, gender transition should be conducted such that a Service member would meet all applicable standards and be available for duty in the birth gender prior to a change in the member’s gender marker and would meet all applicable standards and be available for duty in the preferred gender after the change in gender marker,” the instruction says.

The sex transition phase may prompt a commander to offer the person extended leave or a voluntary absence program or transfer to another command or duty status.

This option was announced after the Joint Chiefs of Staff told Congress they are short the number of troops needed to fully execute the military strategy of fighting a major war.

“When the military medical provider determines that a Service member’s gender transition is complete, and at a time approved by the commander in consultation with the transgender Service member, the member’s gender marker will be changed and the Service member will be recognized in the preferred gender,” the directive orders.

The instruction provides definitions of transgender phrases that commanders have not normally used.

For example, “cross-sex hormone therapy” is defined as the “use of feminizing hormones in an individual assigned male at birth based on traditional biological indicators or the use of masculinizing hormones in an individual assigned female at birth.”

“Real Life Experience” is explained as “the phase in the gender transition process during which the individual commences living socially in the gender role consistent with their preferred gender.”

“Stable in the preferred gender” means that “Medical care identified or approved by a military medical provider in a documented medical treatment plan is complete, no functional limitations or complications persist, and the individual is not experiencing clinically significant distress or impairment in social, occupational, or other important areas of functioning.”

A separate Pentagon memo provides direction on transgender recruits.

If a recruit has a history of gender dysphoria, he or she may not join unless a physician certifies the recruit has completed medical treatment and has been stable for 18 months.

“We have an obligation to provide medically necessary care and treatment to all of our service members in order to keep the force medically ready to deploy,” said Pentagon spokesman Eric Pahon. “We have transgender members in the military services today. We believe that we have the same obligation to them that we have to our other service members. Allowing these transgender individuals to serve openly does not bring new medical problems into the military. It brings these medical problems into the open and enables us to treat them in a way that promotes the readiness of the force.”