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Three Native American men filed a civil lawsuit alleging that the U.S. Indian Health Service failed to protect them from sexual abuse by a pediatrician, Stanley Patrick Weber, in Montana during the 1990s, a federal court filing shows.

The lawsuit filed in the Court of Federal Claims in Washington, D.C., is the first civil action seeking monetary compensation from the U.S. government over Mr. Weber’s growing legacy of sexual abuse of Native American children. His case has shaken the IHS, which provides medical care to 2.6 million tribal members.

“I blame the [IHS] hospital for hiring him,” said one of the plaintiffs, a 35-year-old Montana man who accused Mr. Weber of sexually assaulting him more than a dozen times when he was a child, in an interview. “They just kept their mouths shut because I guess he was a good doctor.” The Wall Street Journal typically doesn’t disclose the names of sexual-assault victims.

The lawsuit filed Wednesday doesn’t detail specific allegations about each man’s contact with Mr. Weber.

Mr. Weber, who worked for the IHS for nearly 30 years before resigning while under investigation in 2016, was convicted in two different courts of sexually abusing six young boys under his care at U.S. hospitals on the Blackfeet reservation in Montana and the Pine Ridge reservation in South Dakota over about two decades. He is serving an 18-year prison term, and is appealing that conviction. He is awaiting sentencing in the second.

The three unnamed plaintiffs in Wednesday’s lawsuit are all members of the Blackfeet tribe in Montana, the lawsuit says. Two plaintiffs, including the man interviewed by the Journal, weren’t among the victims Mr. Weber was convicted of abusing, while the third plaintiff was, according to Peter Janci, their lawyer.

The IHS said in a statement it doesn’t comment on pending litigation. Lawyers for Mr. Weber didn’t respond to inquiries.

Last year, an investigation by the Journal and FRONTLINE showed IHS officials had for decades ignored complaints about Mr. Weber’s conduct, tried to silence whistleblowers and allowed him to continue treating boys despite their suspicions.

That report led to Congressional hearings and at least five federal investigations. The agency said it immediately overhauled how it handles sexual-abuse cases. A White House task force that probed the Weber case and IHS’s broader handling of sex abuse is expected to release recommendations next month on how the agency can further protect its patients.

The 35-year-old man who spoke to the Journal said he first met Mr. Weber in 1993 at age 10, when the doctor examined him. At about that time, medical records viewed by the Journal show, the man, then a 4’8”, 80-pound boy, was admitted to a youth residential center on the Blackfeet reservation known as the Nurturing Center.

In a series of subsequent exams, the man said, Mr. Weber progressed from caressing his legs and ears to touching his genitals and eventually engaging in oral sex. At one point, the man said, Mr. Weber inserted a body part — he wasn’t sure which one — into his anus, saying he needed to check his temperature.

When he protested at one point, the doctor replied: “This is my job to do this,” recalled the man, who now works as a security guard. The man said he never told anyone at the time, except his late mother.

In an account that tracks with other victims’ descriptions to the Journal, the man said he also visited Mr. Weber’s home on the IHS hospital’s grounds, where the pediatrician gave him money and bottles of vodka, and let him play with Teenage Mutant Ninja Turtle figurines.

The new lawsuit cites as its legal basis a treaty with the U.S. government from 1855 to which the Blackfeet tribe is a party. The treaty asserts that “the United States is hereby bound to protect Indians against depredations” and crimes by outsiders.

“There were multiple points along the way where people became concerned about Weber’s behavior, and nobody did anything to protect these boys,” said Mr. Janci, the lawyer, whose firm specializes in sex-abuse cases.

Mr. Janci said his firm began working on the case after the Journal-FRONTLINE report. The suit is seeking $3 million in damages for each plaintiff.

Claims against the government over sexual abuse on Indian reservations have resulted in some significant payouts in the past. For instance, in 2009, a Court of Federal Claims judge ordered the U.S. to pay a woman from the Pine Ridge reservation who accused an army recruiter of sexual abuse nearly $600,000, citing a treaty agreement.

The U.S. Treasury Department pays claims rising from allegations against the government out of a special account on behalf of federal agencies or their employees accused of misconduct. The federal agencies involved don’t have to cover the costs out of their own budget in such cases.

The Indian Health Service’s current leader, Rear Adm. Michael Weahkee, said in September that the agency would provide counseling services for any of Mr. Weber’s victims who reach out, including at private, non-IHS facilities. The three plaintiffs in this suit haven’t done so, their lawyer said.

Update 1/23/20: This story has been updated to include a comment from IHS.