A newly released Justice Department study reports nearly 1 in 10 inmates have experienced sexual violence.
The data, based on a 2008 survey of people who served in state prisons, says the abuse disproportionately hits gay and bisexual inmates. And victims who reported the problems often were retaliated against or ignored, the study said.
The study was released on the same day President Obama decreed that a 2003 law meant to prevent rape in prison protects people in all federal facilities, not just ones overseen by the Justice Department and Federal Bureau of Prisons.
States have up to one year to decide whether to adopt reforms but states that don't follow the new rules could lose 5 percent of federal funds and become ineligible for new grants. California, Oregon and Massachusetts have already made changes.
"No matter how serious the crime an inmate has committed, his or her sentence does not include being raped," said Pat Nolan, president of the Justice Fellowship, which advocates for prisoners.
But Nolan and others raised alarms about whether detainees in immigration facilities, who may not have committed any violent crimes, would receive second class protection under the rape prevention law.
The Department of Homeland Security had fought inclusion under the 2003 law, known as the Prison Rape Elimination Act. NPR has reported on behind the scenes battles over whether the Justice Department could oversee DHS facilities or make rules to cover them.
The White House apparently reached a compromise making clear DHS must follow the law but giving the agency six months to come up with its own rules for doing so.
"DHS has an abysmal track record of preventing and investigating the serious and systemic problems of sexual assault and abuse in its facilities," said Amy Fettig, senior staff counsel at the ACLU National Prison Project.
Rep. Frank Wolf, R - va, a co author of the 2003 law, objected to the delay since rules were supposed to be finished in June 2010.
"I am deeply disappointed that it took so long," he said. "who knows how many rapes could have been prevented if these standards had been put in place sooner. "
A senior Justice Department official said the rule making was one of the most complicated in decades.
The new standards forbid pat downs of female inmates by guards of the opposite sex, require prisons to do more to advise inmates of their rights and services that could help them, and impose audits every three years by an independent overseer. The standards also direct authorities to decide on a case by case basis whether to house transgender inmates in a male or female facility.