Top health officials knew of complaints about a pedophile doctor abusing Native American boys at U.S. Indian Health Service hospitals years earlier than the agency has previously acknowledged, according to an internal investigation the agency released Tuesday after a legal effort by The Wall Street Journal’s publisher, Dow Jones & Co.

The report shows that lawyers at the Department of Health and Human Services, which supervises the Indian Health Service, were notified of allegations against the doctor as early as 2009, and concludes that top regional officials also suspected him of abusing patients. In each instance, officials failed to act and protect children from further abuse by their doctor.

The report examines the career of Stanley Patrick Weber, a pediatrician who worked for the Indian Health Service from 1986 until he resigned amid an investigation into his conduct in 2016. He was later convicted in two separate trials of sexually abusing a total of six boys in his care at IHS hospitals in Montana and South Dakota and was sentenced in 2020 to five lifetime prison terms.

The Journal and FRONTLINE examined the role of the Indian Health Service in covering up Weber’s abuse in the 2019 documentary Predator on the Reservation. The film showed that the federal agency that oversees medical care for 2.6 million Native Americans ignored warning signs of Weber’s abuse, punished whistleblowers and allowed him to continue treating children despite his supervisors’ suspicions.

The report, which the IHS commissioned from a contractor months after the documentary aired, provides new details of the agency’s missteps. Investigators working for the contractor, Integritas Creative Solutions LLC, reviewed thousands of pages of internal IHS records and conducted about 100 interviews that identified “problematic activity within the agency,” said Integritas’s leader, Carl Caulk.

Among the new details: Integritas learned Weber took a teenage Native American boy on a European vacation when he was posted to a civilian hospital in New Mexico on a training assignment in the early 1990s. The investigators also found Weber drafted a memo — and got his boss to sign off on it — at his next assignment, an IHS hospital in Montana, that expanded his duties well beyond pediatrics to potentially include after-school counseling and weekend and overnight trips with children.

“The IHS acknowledges the trauma suffered by the victims of sexual abuse within our agency is unacceptable,” the agency said in a statement provided by spokeswoman Jennifer Buschick. “These actions are reprehensible, and we sincerely regret the harm caused to those involved,” the statement, which pledged improvements, said.

The report was completed in January 2020, but the IHS declined to release the document or publicly discuss its findings, citing a law that makes certain medical quality assurance records confidential. Dow Jones & Co. and the New York Times both filed lawsuits seeking to compel the government to disclose the report under public records laws in April 2020. The news organizations argued that an investigation into managerial missteps that allowed a sexual predator to flourish didn’t constitute an assessment of medical quality.

A district court ruled IHS must release the report in January, but the government appealed. A three-panel judge affirmed the lower court’s ruling this past week, leading to Tuesday’s disclosure.

Read more: Government Must Release Report About Indian Health Service Predator, Court Rules

Some managers were singled out in the report for their handling of complaints about Weber, such as Bill Pourier, the CEO of the Pine Ridge hospital in South Dakota while Weber worked there in the 2000s, and Mary Ellen LaFromboise, who oversaw the Blackfeet Community Hospital in Browning, Mont., when Weber was assigned there.

The report found that Ms. LaFromboise, despite receiving credible complaints from staff members, “did nothing to document the complaints, investigate internally as to their validity, refer the matter to law enforcement or suspend or remove Weber” from the hospital. Mr. Pourier, it found, consistently gave Weber high marks in performance reviews despite harboring suspicions about Weber and “treated an allegation of child abuse as an inconvenient personnel issue.”

The report shows that lawyers at HHS were notified of the allegations about Weber at the Pine Ridge hospital in March of 2009 after another doctor complained about his conduct to Mr. Pourier and another IHS manager. The heavily redacted portion of the report shows the lawyers recommended that the hospital form an “ad hoc Investigation Committee” to review the allegations internally. The report doesn’t say whether they advised the agency’s officials to refer the matter to law enforcement, as required by law.

Mr. Pourier didn’t respond to a request for comment and Ms. LaFromboise couldn’t be reached.

The report also details efforts by IHS leaders to improve the agency’s safeguards for preventing sexual abuse by its employees. After the Journal and FRONTLINE’s initial report, the agency overhauled its policies and faced multiple federal investigations, including one by a White House task force that made additional recommendations.

The report recommended that the agency go further, enhancing reporting requirements and reviewing its human resources practices. Agency officials at all levels failed to document complaints, couldn’t retrieve files when needed and didn’t communicate with one another at critical times, the consultants found.

For instance, the witness who recalled Weber’s European vacation with his teenage companion says she later told an IHS official who contacted her for a job reference about her concerns over his inappropriate behavior with adolescent boys, but the report said IHS never documented it.

The report also detailed how Dr. Dan Foster, an IHS psychologist at Blackfeet, repeatedly registered concerns about Weber’s behavior to both Ms. LaFromboise and Dr. Randy Rottenbiller, the chief medical officer, as well his own supervisor in the Billings Area Office, Margene Tower. Ms. Tower, now deceased, tried to handle the situation “diplomatically,” Dr. Foster told investigators.

Ms. LaFromboise told investigators that she and Dr. Foster eventually alerted the Billings Area office of the accusations against Weber during a phone call, threatening to kick Weber off the reservation if something wasn’t done. The official whom she and Dr. Foster said they reached out to subsequently told investigators he did not remember such a call.

According to the report, Dr. Rottenbiller was told by the area director in 1995, whose name is redacted, that the director had conducted his own review of Weber and received a complaint from a parent about Weber, and told Dr. Rottenbiller to fire him. The former area director refused to be interviewed by Integritas and said he couldn’t recall the meeting with Dr. Rottenbiller. He also asserted to investigators that no allegations about Weber ever got to him and that he would have been sensitive to any accusations of sexual abuse of children had he received them.

The enabling of Weber’s predatory actions wasn’t an isolated failure, the consultants found.

One such example was that of Dr. Frankie Delgado, whom the agency transferred to the IHS hospital on the Cheyenne River-Eagle Butte Indian Reservation in South Dakota after repeated accusations of sexual harassment and attempted assault in Pine Ridge, where he was the medical director. Dr. Delgado was one of the officials who approved Weber’s continued employment after child sexual abuse allegations emerged in 2009, the report said.

While working in Eagle Butte in 2011, Dr. Delgado was indicted by a federal grand jury on multiple counts of abusive sexual contact committed against two nurses. He was allowed to plead guilty to misdemeanor disorderly conduct in exchange for the dismissal of the felony charges, the report says. From there he went on to work for the Department of Veterans Affairs, which was aware of his guilty plea when it hired him, the report said.

Dr. Delgado couldn’t be reached for comment Tuesday.

— Jennifer S. Forsyth contributed to this article.

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