A U.S. Indian Health Service doctor was indicted Thursday on charges of sexually abusing his Native American patients at a health center in South Dakota, deepening a crisis over the handling of sexual misconduct that has consumed the federal agency for a year.

The doctor, Pedro Ibarra-Perocier, a family medicine physician, was indicted on eight counts of sexual abuse involving four different adult patients at the agency’s clinic on the Yankton Sioux Reservation, in the town of Wagner in the southeastern corner of the state.

A lawyer for Dr. Ibarra-Perocier declined to comment. A U.S. District Court clerk in Sioux Falls said he had pleaded not guilty.

The IHS’s broader sex-abuse crisis began with revelations about another IHS doctor, Stanley Patrick Weber, who was sentenced on Monday to five lifetime prison terms for sexually abusing Native American boys in his care at the agency’s Pine Ridge, S.D. hospital.

The IHS mishandled accusations about Weber dating back to the early 1990s, an investigation last year by The Wall Street Journal and the PBS series Frontline showed. Officials transferred him between hospitals after he fell under suspicion for sexually abusing boys, ignored warning signs and punished whistleblowers who accused Weber until the pediatrician finally retired in 2016, in the face of a federal probe.

For more than two decades, government pediatrician Stanley Patrick Weber raised suspicions that he was a pedophile. The Wall Street Journal and Frontline investigate how the Indian Health Service doctor was transferred from reservation to reservation and allowed to continue to treat children despite accusations he was sexually abusing Native American boys. Photo composite: Adele Morgan and Mike Shum/Frontline/WSJ

After the Journal and Frontline’s report, the agency overhauled its policies for preventing sexual abuse and protecting patients, but a government watchdog has said the changes don’t go far enough.

“Patients and employees of the Indian Health Service should never face sexual harassment or abuse,” a statement provided Thursday by an IHS spokeswoman said. “We will continue to institute the reforms necessary to create the high quality care environment that our patients and employees should expect in our clinics and hospitals,” the statement said.

Sen. John Hoeven (R., N.D.), chairman of the Senate Committee on Indian Affairs, said Thursday he expected the agency to brief lawmakers on Dr. Ibarra-Perocier’s actions and its response to them. Lawmakers have “made it clear that IHS needs to address patient abuse and employee misconduct,” he said.

In late 2018, Dr. Ibarra-Perocier was removed from his duties at the Wagner clinic and escorted out of the facility after one of the women he treated complained that he had abused her, people close to the agency said. A worker at the facility reported that incident to law enforcement, the people said.

The agency launched an internal investigation at that time, the people said, and placed the doctor on administrative leave. But in April of last year, Dr. Ibarra-Perocier was allowed to return to work at the agency’s administrative offices in Aberdeen, S.D., the people said.

Agents from the Federal Bureau of Investigation and the Department of Health and Human Services’ Office of Inspector General meanwhile identified the additional women who complained about Dr. Ibarra-Perocier’s conduct in the exam room, people familiar with the matter said.

The charges don’t describe the exact nature of the complaints about Dr. Ibarra-Perocier. They allege he caused his patients “to engage in a sexual act by threatening and placing [the victims] in fear,” and coerced them into sexual contact.

The new allegations aren’t the first about Dr. Ibarra-Perocier, some of the people familiar with the matter said. At least two nurses accused him internally of workplace sexual harassment in past years, the people said. Dr. Ibarra-Perocier’s wife, who left her job due to illness in 2017 and died the next year, was his supervisor during that time, they said.

In December, the HHS inspector general found the agency’s patient-protection policies don’t go far enough.

The inspectors concluded the agency had focused so narrowly on medical providers who commit child sexual abuse that it didn’t adequately direct employees on how to respond to other kinds of perpetrators, victims or types of abuse.

A separate White House task force convened to examine the widening scandal is expected to release additional recommendations for improving safety at the agency’s facilities next week.

The IHS also commissioned a review of its own handling of the Weber case that is expected to lead to additional changes. The private contractor the agency retained to do that work completed its report, but the agency has withheld the document, arguing that it is a record of quality assurance program that by law is confidential.

“IHS is committed to transparency, accountability and continuous improvement,” an agency spokeswoman said in a January statement. “We also respect and protect patient privacy.”

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