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A U.S. government pediatrician convicted of sexually abusing Native American boys under his care is still receiving his government pension, officials said, and records indicate he is due more than $1.8 million during his prison term.

The government likely can’t stop the pension payments to Stanley Patrick Weber, unless Congress changes federal law.

Mr. Weber worked at federal Indian Health Service hospitals for about 30 years. He was convicted in September of sexually abusing two boys on a reservation in Montana and faces another trial over allegations he sexually assaulted four more in South Dakota. The abuse occurred while the pedophile doctor was on duty at the government hospitals or in his government-provided homes. He has appealed his conviction and pleaded not guilty ahead of the other trial.

Officials who oversaw Mr. Weber transferred him from one reservation to another when complaints about his conduct arose and ignored repeated warnings from whistleblowers, according to a recent investigation by The Wall Street Journal and FRONTLINE. On Tuesday, the Trump administration said it would convene a task force of law enforcement and other government officials to examine why the IHS failed to stop Mr. Weber and how better to protect Native American children under the care of the health agency.

Now, government officials are poised to continue paying him his retirement package whether they like it or not, they said.

A federal judge in January sentenced Mr. Weber to 18 years and 4 months in prison. If he serves the full term, the government would pay him around $1.8 million during his incarceration, not including the impact of any future cost-of-living adjustments that can increase pension pay.

Mr. Weber, who is 70 years old, is now collecting an annual pension he is due to receive for life as a former captain in the U.S. Public Health Service Commissioned Corps. It is now worth about $100,000 a year, according to an estimate by the Journal and FRONTLINE. The estimate is based on a review of military pay tables and information about Mr. Weber obtained in public-records requests. Military-pension experts and officials familiar with the former pediatrician’s career reviewed the Journal’s calculations.

The Public Health Service provides a pipeline of doctors, nurses and other professionals to its sister agencies within the government, including the IHS. Its commissioned officers wear military-style dress uniforms and share a system of ranks with the U.S. Navy.

Mr. Weber retired from the Public Health Service at the end of 2011 after 25 years, personnel records show. That came on top of a prior stint in the Army for a combined 30 years of active duty. He continued working for the IHS as a civilian employee until 2016, civilian payroll records show.

“Since Dr. Weber was convicted in September 2018, the Commissioned Corps has been in frequent contact with HHS Office of the General Counsel to determine what actions, if any, could be taken to stop him from receiving his retirement pay,” said a spokesman for the Department of Health and Human Services, which runs both the IHS and Public Health Service.

“This is a unique complex situation,” the statement said. “Nonetheless HHS is looking in every corner of relevant existing laws and policies to determine what possible options may be available.”

An IHS official said meetings about stopping Mr. Weber’s pension began the day after he was convicted.

While the government can cut off pensions when current military or other uniformed employees like Public Health Service officers are convicted of crimes, the options are much more limited when misconduct comes to light only after a retirement, military lawyers say.

Under such circumstances, “no misconduct short of one thing, treason, can result in the forfeiture of a pension,” said Mark Sullivan, a North Carolina-based family lawyer and former Army Reserve colonel. “Atrocities are not a reason for forfeiture,” he said.

Mr. Weber has a net worth of more than $1 million as of late last year, in addition to his pension, according to prosecutors. His defense attorney is Harvey Steinberg, a top Denver lawyer who is known for defending sports stars including National Football League players.

Mr. Steinberg and an associate didn’t respond to a request for comment.

Mr. Weber is in custody in the county jail in Rapid City, S.C.

Public Health Service personnel, along with the Indian Health Service’s civilian managers, oversaw Mr. Weber at key times in his career. One superior in his chain of command when the government investigated him in 2009 was Ron Keats, a Public Health Service captain. Mr. Weber was cleared during the probe. However, about a year later, federal agents confiscated thousands of images of child pornography from Mr. Keats. He was subsequently convicted on related charges.

In that case, the Public Health Service has so far avoided paying Mr. Keats’s pension. Officials denied Mr. Keats’s request for voluntary retirement after the child pornography was discovered, and declared him “absent without leave” after he was incarcerated, according to a health department memo from the time. Health officials later cited his AWOL status as a reason to terminate his commission and deny retirement benefits.

Mr. Keats, 61, sued the U.S. government in an effort to recover his pension. The case is pending.

“There’s no regulation in the Public Health Service that gives them any authority to withhold their pension,” said Mr. Keats’s lawyer, Jim Klimaski. “There just isn’t any law.”

The Department of Health and Human Services declined to comment on the number of pensions the Public Health Service has withheld.

Lawmakers in recent years have put forward several proposals to limit pension payments to federal employees implicated in misconduct, but have gained little traction, said Jason Briefel, director of government affairs at employment-law firm Shaw Bransford & Roth.

One exception, Mr. Briefel said, is a 2017 law that empowers the Department of Veterans Affairs to claw back a portion of VA employees’ pensions when they subsequently are convicted of felonies related to their work. But it doesn’t apply to other branches of the government. A 1950s-era law gives the government the ability to recoup pensions of retirees involved in some national-security related crimes.

The Public Health Service shares its pension system with the military. A person of Mr. Weber’s rank history and 30-year tenure earned about $10,000 a month in base pay in 2011. Someone retiring under those circumstances would get 75 percent of that as their starting pension. Retirees can get annual cost-of-living increases to their pensions on top of that. Military physicians also receive incentive pay and bonus pay that makes their incomes more competitive with civilian workers, but isn’t factored into pension calculations.

Curt Sheldon, a retired Air Force pilot and financial planner, said a client with a similar service history who recently retired also received a roughly $100,000 pension. Various factors could alter the final math, he said, but “it may change a few dollars one way or the other.”

Marion Four Horns, the mother of a man Mr. Weber was convicted of assaulting as an 11-year old boy in the mid-1990s in Montana, said she was angered that the former pediatrician continued to receive a pension. “I don’t feel like Weber has paid enough for all the kids he has traumatized,” Ms. Four Horns said. “And now he’s getting money?”