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The U.S. Indian Health Service has overhauled sex-abuse reporting practices at a troubled North Carolina substance-abuse treatment center the agency runs after allegations its managers mishandled a 2016 incident.

In June, The Wall Street Journal reported that leaders at the Cherokee, N.C. facility and the regional office overseeing it botched the response to allegations that a maintenance worker may have engaged in sexual misconduct with a teenage patient, which the maintenance worker denied.

A supervisor at the facility, Unity Healing Center, told employees not to report their suspicions to law enforcement, as required under U.S. law, and no one did so until another worker broke ranks seven months later, the Journal reported. Other workers said they had been trained to bring such concerns to managers, not the police.

Now, the agency’s Nashville-based regional leader has told employees that they shouldn’t defer to managers about whether to make such reports.

“While an individual who is making a report is asked to notify his or her supervisor, a supervisor does not serve in the capacity as a deciding or approving official,” Beverly Cotton, the regional official, said in a June 26 memo to her subordinates, which has been reviewed by the Journal.

Dr. Cotton’s memo to employees didn’t specifically mention anything about sexual misconduct, instead broadly speaking of “fraud, waste, abuse and mismanagement.”

However, in a statement to the Journal on Monday, Dr. Cotton, who has a doctorate in nursing, said she sent “a clear message that employees should report mismanagement which was a concern voiced by former employees of Unity in the WSJ article.”

The Journal report, citing former employees and internal documents, examined an incident, which was caught on surveillance video, in which a 47-year-old maintenance man entered a private bathroom alone with a 16-year-old Unity patient. The man had been accused by other workers of inappropriate conduct with the girl, including hand-holding and hugging, in the weeks before, the Journal reported. Hours after two staff members questioned the girl about the incident, she attempted to hang herself, the Journal reported.

The maintenance man, Nathaniel Crowe, didn’t respond to requests for comment Monday. In a Facebook post last month, he said he had been fully cleared and dismissed allegations about him as “a total misconception.”

In a meeting last month at a conference of tribal officials, the agency said its written child-abuse reporting policies at Unity had been revamped and were awaiting approval from higher-ups, according to a slide deck of Dr. Cotton’s presentation at the meeting that was provided by the IHS.

Officials notified family members of patients and referring agencies of the Journal report, according to the slide deck.

Dr. Cotton told leaders gathered at the United South and Eastern Tribes conference in Nashville that the agency was reviewing whether appropriate actions were taken at Unity and whether there was “an environment that prevented staff from reporting a suspicion of sexual abuse,” the presentation said.

However, Dr. Cotton denied to tribal leaders at the recent meeting that any sexual misconduct has been substantiated, people who attended said. A federal investigation of incident is ongoing, law-enforcement officials said.

The IHS also last week ordered employees agencywide to complete a training focused on sex-abuse reporting.

That training discussed the implementation of new policies put in place after a report by the Journal and FRONTLINE in February that detailed mishandled sex-abuse allegations against an IHS pediatrician stretching back more than two decades. The doctor was convicted in September of sexually assaulting some of his patients.

In the training, the agency lists warning signs of sexual abuse, such as grooming of potential victims, according to a copy of the material. It directs employees to make reports of any suspected sex abuse to local and federal law enforcement within 24 hours.