A decade after President George W. Bush signed into law the Prison Rape Elimination Act, sexual abuse is still rampant in America’s corrections facilities, with a growing number of accusations lodged against the very officers charged with protecting their inmates.

Nearly half of all sexual assault accusations reported in U.S. correctional facilities in 2011 were aimed at prison guards or staff, according to a report released Thursday by the Justice Department’s Bureau of Justice Statistics. That was up 18 percent since 2006.

But the challenge for officials is sorting through cases in which evidence indicates the commission of a crime and those in which prisoners may have been motivated solely by a desire to harm guards they don’t like — a concern corrections unions have raised for years. The report found that only about 10 percent of reported sexual assaults in prison could be substantiated.

Among the accused perpetrators, less than half were prosecuted and 22 percent remained in their jobs, the report said.

“An inmate is just as threatened by staff as … by other inmates — this wasn’t the prevalent thought just a few years ago,” said Jamie Fellner, who served on the National Rape Elimination Commission that was created by Congress to better understand the dynamics of sexual assaults behind bars.

In 2009, that panel released a number of recommendations on how to better protect and defend victims of sexual assault.

Ms. Fellner said the statistics suggesting a growing number of officer-on-inmate abuse point to either a culture of sweeping such attacks under the rug or just poor prison management.

The number of reported incidents may be grossly underrepresented by official statistics, other analysts warn.

“This report really captures only a very small percentage of the sexual abuse that goes on in prisons,” said Chris Daley, deputy director of Just Detention International, a human rights organization aimed at stopping sexual abuse in prisons. “And, sadly, for only a very small percentage, was there any real justice.”

The statistics, which are gathered by the Justice Department, track reports that have been formally documented by U.S. correctional institutions. In order to be recorded, a victim must come forward and be identified without fear of retaliation, a significant hurdle for most victims, Mr. Daley said.

The report found a 12 percent rise in all allegations of sexual victimization in prison from 2009 to 2011, with 8,763 total complaints. Mr. Daley estimates that number is way too conservative, placing the number of sexual assaults at about 200,000 annually.

“It’s a big deal for an inmate to file a report, especially if it’s against staff,” Mr. Daley said. “They have to have some sense that something will come out of it, and there’ll be no retaliation.”

Mr. Bush in 2003 signed a bill passed by a Congress alarmed about the epidemic of prisoner-on-prisoner assaults. Since then, news headlines, like the new statistics, have pointed toward more attacks committed by prison staff.

This month, a Milwaukee County jailer was accused of raping a 26-year-old female inmate and then covering it up. Milwaukee County Sheriff David A. Clarke has ordered a criminal investigation.

Last year, a New York female correctional officer was charged with raping a male inmate in a maximum-security state prison in the Hudson Valley. She later was found pregnant with his child.

In Utah, a female inmate who won a $1.4 million civil lawsuit and a criminal conviction against a corrections officer who raped her was found dead in her cell back in 2012, raising concerns about retaliation.

These types of stories will stop with better leadership in the corrections industry, public officials who don’t tolerate abuses, increased community outrage, and successful litigation on the behalf of victims, Ms. Fellner said.

“Prisons that are badly run have a higher prevalence of sexual abuse,” she said. “Forceful, committed management, that has put in place effective policies that do not tolerate sexual conduct by staff will see fewer cases, period. Sexual abuse flourishes when there’s bad management.”

Mr. Daley sees change on the horizon. It wasn’t until last year that the Department of Justice accepted and implemented some of the recommendations and regulations the National Rape Elimination Commission suggested in 2009.

“We really are now at a place where the meat of the law is being implemented in facilities around the nation,” he said. “We don’t yet know how effectively these regulations are being implemented, but we do know that they’re the best tool we have to end sexual abuse.”

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