This article is a joint investigation between Frontline PBS and The Wall Street Journal. A related documentary aired Feb. 12 on PBS.

At first, officials at the U.S. Indian Health Service overlooked the peculiarities of their unmarried new doctor, including the children’s toys he hoarded in his basement on the reservation. They desperately needed a pediatrician at their hospital in Browning, Mont.

By 1995, after three years, they became convinced Stanley Patrick Weber was a pedophile and pushed for his removal from the government-run hospital.

“You’re going to have to leave,” Randy Rottenbiller , its clinical director at the time, recalled telling the doctor after learning a child patient had stayed the night in his house.

Stanley Patrick Weber in a 1990s passport photo, submitted as evidence by prosecutors in Montana.

But the Indian Health Service didn’t fire Mr. Weber. Instead, it transferred him to another hospital in Pine Ridge, S.D. He continued treating Native American children there for another 21 years, leaving behind a trail of sexual-assault allegations.

Many of his known and alleged victims have since struggled with addiction and have moved in and out of prison. As boys, they were especially vulnerable and troubled. They lived in some of America’s poorest communities, isolated and desolate places where health problems are rampant and basic services such as grocery stores are scarce.

An investigation by The Wall Street Journal and the PBS series Frontline found the IHS repeatedly missed or ignored warning signs, tried to silence whistleblowers and allowed Mr. Weber to continue treating children despite the suspicions of colleagues up and down the chain of command.

The investigation also found that the agency tolerated a number of problem doctors because it was desperate for medical staff, and that managers there believed they might face retaliation if they followed up on suspicions of abuse. The federal agency has long been criticized for providing inadequate care to Native Americans.

After a tribal prosecutor outside of the IHS finally investigated his crimes, Mr. Weber was indicted in 2017 and 2018 for sexually assaulting six patients in Montana and South Dakota. Court documents and interviews with former patients show that Mr. Weber plied teen boys with money, alcohol and sometimes opioids, and coerced them into oral and anal sex with him in hospital exam rooms and at his government housing unit.

“IHS, the local here, they want to just forget it happened,” said Pauletta Red Willow , a social-services worker on the Pine Ridge reservation. “You can’t ever forget how someone did our children wrong and affected us for generations to come.”

In an interview, Rear Adm. Michael Weahkee , an officer in the U.S. Public Health Service Commissioned Corps and the acting head of the IHS, expressed sorrow over the agency’s failures and promised an investigation into how Mr. Weber was able to prey on children under the agency’s care. “We really want to mitigate the possibility of anything like this ever happening again,” said Adm. Weahkee.

In 2006, teenagers assaulted Mr. Weber in his house on the Pine Ridge reservation. Photo: Mike Shum/Frontline/WSJ

Mr. Weber, 70 years old, told investigators he never had sex with his patients, according to a recording of a law-enforcement interview in May 2016. He was convicted in September of sexually assaulting two Montana boys—a verdict he is appealing—and sentenced to 18 years in prison. He faces another federal trial later this year in Rapid City, S.D. He lost his medical license. He and his lawyers declined to comment for this article.

The IHS provides medical care for 2.3 million Native Americans, many of whom have no other access to health care. Because the agency has struggled to recruit medical staff and experienced leaders, especially at remote reservations, officials said they gave second chances to doctors who likely would have struggled to find work elsewhere. This includes some with histories of drug problems, criminal convictions and violence, the Journal-Frontline investigation found.

Most Vulnerable People living on Indian reservations face higher levels of poverty and health challenges. U.S. national rate Pine Ridge reservation Blackfeet reservation Alcohol use disorders mortality rate, 2014 Poverty rate, 2017 14.6% 2.9 deaths per 100,000 25.8 50.4 35.8 20.7 Life expectancy, 2014 Unemployment rate, 2017 6.6% 79.1 years 20.2 66.8 10.2 73.6 Lowest of any county in U.S. Blackfeet reservation U.S. national rate Pine Ridge reservation Alcohol use disorders mortality rate, 2014 Poverty rate, 2017 2.9 deaths per 100,000 14.6% 25.8 50.4 35.8 20.7 Unemployment rate, 2017 Life expectancy, 2014 6.6% 79.1 years 20.2 66.8 10.2 73.6 Lowest of any county in U.S. Pine Ridge reservation Blackfeet reservation U.S. national rate Alcohol use disorders mortality rate, 2014 Poverty rate, 2017 14.6% 2.9 deaths per 100,000 25.8 50.4 35.8 20.7 Life expectancy, 2014 Unemployment rate, 2017 6.6% 79.1 years 20.2 66.8 10.2 73.6 Lowest of any county in U.S. U.S. national rate Pine Ridge reservation Blackfeet reservation Poverty rate, 2017 14.6% 50.4 35.8 Unemployment rate, 2017 6.6% 20.2 10.2 Life expectancy, 2014 79.1 years 66.8 73.6 Lowest of any county in U.S. Alcohol use disorders mortality rate, 2014 2.9 deaths per 100,000 25.8 20.7

“It’s fair to say that because of the absolute need to fill positions, we don’t really get the best of the best,” said Bob McSwain , a former director of the agency. “There’s a strange tolerance level that, ‘Oh, OK, the guy’s a womanizer, the guy’s this, the guy’s that, but he comes in to see patients,’ ” he said.

One of Mr. Weber’s victims, testifying in Montana, described the doctor sexually assaulting him on a hospital examination table when he was about 11, around the time his father had killed himself.

Joe Four Horns in 1994, on left, around the time Mr. Weber sexually assaulted him, in a photo submitted by prosecutors. Mr. Four Horns, on right in a Facebook photo, is now serving a prison sentence for bank robbery.

Joe Four Horns in 1994, around the time Mr. Weber sexually assaulted him, in a photo submitted by prosecutors in Montana.

“It’s in my mind every day. I got molested. I got—I was a little boy,” testified Joe Four Horns , now a convicted bank robber.

Another former patient testified that the doctor had inserted a finger into his anus in an IHS exam room when he was about 8 years old. The doctor used two fingers on his next visit, and later, his penis. The man, now age 32, said in an interview he learned years later he wasn’t Mr. Weber’s sole victim. Others in his circle of friends were also assaulted and sometimes swapped stories about it at drunken gatherings, he said. He said the incidents ruined his life.

The Journal doesn’t disclose the names of sexual-assault victims without their permission.

Mr. Weber, known as Pat, got his start in medicine as a Green Beret medic. After finishing medical school in 1983, he joined the IHS and worked in Oklahoma and New Mexico before landing in Browning, the seat of the Blackfeet reservation, in 1992.

The hospital’s CEO at the time, Mary Ellen LaFromboise , said she initially welcomed Mr. Weber. “We had been without a pediatrician for a while,” she said.

She said she overlooked some initial suspicions about Mr. Weber. Her personnel director said she saw him hanging out with boys at a Pizza Hut. One doctor said that Mr. Weber told him he had arrived in Browning early so he could arrange a camping trip with his future patients.

Mr. Four Horns, pictured in a Facebook photo, is now serving a prison sentence for bank robbery.

Mr. Weber was assaulted by a relative of a boy who was upset the youngster was spending time at the doctor’s house, according to Ms. LaFromboise. By that time, some administrators said they concluded he was a pedophile.

Ms. LaFromboise wasn’t so sure, she said, but agreed she had to act. She said she didn’t know of any IHS doctor “who was ever fired, even if they had problems.” She alerted IHS regional officials.

An official there ordered Dr. Rottenbiller, Mr. Weber’s boss at the time, to remove him from the Browning hospital. Dr. Rottenbiller said when he confronted Mr. Weber, the pediatrician replied he was planning to leave anyway after receiving threats.

On June 8, 1995, soon after he left Montana, Mr. Weber reported for work at the Pine Ridge IHS hospital, personnel records show.

More than half of the population of the Pine Ridge reservation lives in poverty. The life expectancy is lower than in any other county in the country. VIDEO: MIKE SHUM/FRONTLINE/WSJ

In his first months on the job, a parent complained about Mr. Weber’s conduct, said Sara Dye, then the top doctor at IHS’s South Dakota regional office.

Hospital staff referred the matter to law enforcement, Dr. Dye said, and reassigned Mr. Weber to administrative duties. A Federal Bureau of Investigation inquiry didn’t lead to charges, a person familiar with the matter said. Mr. Weber was returned to normal work, Dr. Dye said.

Kathey Wilson , an IHS manager at Pine Ridge at the time, said she had learned that Mr. Weber had been investigated in Browning. He was allowed to practice anyway, she said, because he had never been charged or convicted. She declined to answer additional questions.

In Pine Ridge, whispers spread about the teenage boys who frequently visited his home. Mr. Weber later told investigators he simply hired them for garden chores. Nurses said he checked boys into the hospital room farthest from their station.

One of Mr. Weber’s patients, now a 31-year-old South Dakota state inmate, said in a series of interviews that the pediatrician molested him in the hospital’s exam rooms starting in the late 1990s, when he was about 11 years old.

Reservations such as the one that encompasses Browning, Mont., are some of America’s poorest communities, and many boys living there are especially vulnerable or troubled. Photo: Mike Shum/Frontline/WSJ

When his head was cut open in a fight, the inmate said, Mr. Weber stitched him up at his house and gave him a bottle of narcotic pain medicine. After that incident, the doctor often used pain pills and money to coerce him into sex, the inmate said.

Late on the night of Nov. 14, 2006, the inmate said, he decided to enact revenge. He and two other teenage boys knocked on Mr. Weber’s door with shirts tied around their faces. When Mr. Weber cracked the door, one of the boys, Henry Red Cloud , kicked it in, bashing Mr. Weber in the face. They battered the doctor and stole a couple hundred dollars, Mr. Red Cloud said.

The inmate said it was payback for “what I was put through.”

A third man present that night eventually testified that Mr. Weber sexually assaulted him, too, saying Mr. Weber invited him to his home to help clean up his basement, gave him beer and asked him to perform oral sex on him. Then a 13-year-old boy, he complied and left with $100, he said in court.

Bill Pourier , CEO of the Pine Ridge IHS hospital from 2003 to 2011, said in an interview he found Mr. Weber sitting on a gurney in the emergency room the night of the assault, his face bloodied. The doctor refused to answer his questions or talk to law enforcement, Mr. Pourier said.

Rear Adm. Michael Weahkee is the current head of the IHS. Photo: Mike Shum/Frontline/WSJ

Mary Ellen LaFromboise ran an IHS hospital in Montana where Mr. Weber worked. Photo: Mike Shum/Frontline/WSJ

Mr. Pourier said his boss in the agency’s regional office in Aberdeen, S.D., required him to seek her permission to contact law enforcement about any concern. He said he asked to do so after Mr. Weber’s incident, but never heard back.

Asked whether he should have stepped outside the chain of command to contact police, Mr. Pourier said, “I couldn’t afford to take the risk at that time to lose my job.”

The Journal was unable to reach Mr. Pourier’s immediate boss at the time. The current IHS director, Adm. Weahkee, said management should never bar anyone from reporting potential misconduct to law enforcement.

On Dec. 2, 2008, Mark Butterbrodt , another pediatrician at Pine Ridge, contacted the South Dakota medical board alleging that Mr. Weber “selectively cherry-picks young teenage boys in clinic,” according to a copy of the complaint described to the Journal and Frontline. The board investigated. It declined to comment on its findings.

The following year, Dr. Butterbrodt documented the allegations in a letter to his IHS bosses, including Jan Colton , then the hospital’s clinical director. She appointed a panel to investigate. “There were suspicions, but they could find no hard evidence,” said Dr. Colton, a dentist who is now retired.

The IHS suspended Mr. Weber around this time and referred the matter to Ronald Keats , a regional IHS administrator. When the IHS investigation turned up nothing, Mr. Weber returned to work, according to Mr. Pourier.

Mark Butterbrodt documented his allegations against Mr. Weber in a letter to his IHS bosses. (Passages highlighted by the Journal.)

About a year later, Mr. Keats himself was arrested on child-pornography charges. The investigation revealed he had stored sexually explicit images of children on a compact disc found in an elevator of his government office building. He was convicted in 2012 of possessing child pornography. Mr. Keats didn’t respond to requests for comment.

After a clash with Mr. Weber, Dr. Butterbrodt was pulled into a supervisor’s office and, within weeks, transferred to a remote facility in North Dakota and stripped of bonus pay, which amounted to around one-third of his annual salary, according to personnel records and Dr. Butterbrodt.

“I was chased off by a pedophile and the people who chose him over me,” said Dr. Butterbrodt, who retired soon after.

The agency’s then-top regional doctor in Aberdeen, Rod Cuny , said he reviewed Dr. Butterbrodt’s transfer in 2011 and concluded he had been unfairly punished. Dr. Cuny said he also followed up on questions about Mr. Weber’s conduct. Relying on the earlier findings of the agency’s 2009 internal probe that cleared the doctor, however, he dropped it.

Dr. Cuny said many IHS hospitals suffered from a weak medical staff, in which problem doctors were asked to police one another. When a hospital CEO wanted to hire an Oregon emergency-room doctor in 2013, Dr. Cuny said, he learned from his staff that the doctor, John F. Lindberg , had testified in court that he had sex with an underage prostitute. Dr. Lindberg said he thought the prostitute was 19 years old.

Mr. Weber arrived at federal court in Rapid City, S.D., on Nov. 1, 2017, for a hearing after he was indicted on sexual-assault charges. Photo: Kristina Barker for The Wall Street Journal

“I just held back and went ahead and gave this guy a second chance,” Dr. Cuny said. Dr. Lindberg didn’t respond to requests for comment.

The IHS also hired a family-practice doctor who had previously been barred from the agency after inappropriately doling out narcotic pain pills, and a doctor who previously had been convicted of several crimes including exposing himself to a teenage girl, according to regulatory and court records.

Adm. Weahkee said managers should prioritize protecting patients over filling slots.

Dr. Butterbrodt made one last effort to oust Mr. Weber. He said he called Wehnona Stabler , then the new CEO at the Pine Ridge IHS hospital, and made an anonymous complaint.

Ms. Stabler said in an April 2017 email to the Journal that she remembered the call about Mr. Weber, but the complainant didn’t follow up with specifics.

Two months after that email, Ms. Stabler was indicted in federal court for accepting a $5,000 gift in 2013 from Mr. Weber that she didn’t report on a government ethics form. She pleaded guilty and was sentenced to a year of probation. She didn’t respond to requests for comment about the gift.

In 2015, Mr. Weber was finally tripped up—not by IHS officials contacting law enforcement, but by tribal investigators.

Elaine Yellow Horse , then a tribal prosecutor, decided to look into the case after an unrelated sex-crimes case reminded her of allegations she had heard years earlier from Dr. Butterbrodt. She identified a potential victim of Mr. Weber’s—the inmate who had participated in the assault on him—and her boss contacted federal agents, according to tribal investigative records.

Elaine Yellow Horse, a tribal prosecutor, decided to look into allegations against Mr. Weber. Photo: Mike Shum/Frontline/WSJ

The inspector general of the Department of Health and Human Services, which runs the IHS, opened a criminal investigation. In May 2016, local IHS officials tipped off Mr. Weber that he was being investigated, the doctor later told law-enforcement interviewers. He resigned the following Sunday evening, effective the next day.

Following Mr. Weber’s conviction last September in Montana, the Journal and Frontline sent the IHS written questions about the agency’s handling of the matter. Two weeks later, officials began seeking an outside contractor to investigate Mr. Weber’s three decades at the agency.

“If there are individuals who were aware that something was going on” but didn’t speak up, Adm. Weahkee said, “then you’re basically culpable and complicit in those actions.”

Some officials who crossed paths with Mr. Weber say they are haunted by that possibility.

“One of the feelings I had was of somebody coming up to me and saying, you didn’t protect me,” said Ms. LaFromboise, the former Browning hospital CEO. “You hired him, he worked in your hospital, and you let him do things to us.”

The IHS has ordered an independent review of Mr. Weber’s three decades at the agency, including his time in Browning, Mont. VIDEO: MATTHEW STAVER/FRONTLINE/WSJ

—Lisa Schwartz contributed to this article.

Write to Christopher Weaver at christopher.weaver@wsj.com and Dan Frosch at dan.frosch@wsj.com