Indian reservations have for years grappled with chronic rates of crime higher than all but a handful of the most violent U.S. cities. But the Justice Department, which...

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Indian reservations have for years grappled with chronic rates of crime higher than all but a handful of the most violent U.S. cities. But the Justice Department, which is responsible for prosecuting most violent crimes on reservations, files charges in only about half of Indian Country murder investigations and turns down nearly two-thirds of sexual assault cases, according to new federal data.

The country’s 310 Indian reservations have violent crime rates that are more than 2 1/2 times higher than the national average, according to data compiled by the Justice Department. American Indian women are 10 times as likely to be murdered than other Americans. They are raped or sexually assaulted at a rate four times the national average, with more than 1 in 3 having either been raped or experienced an attempted rape.

The low rate of prosecutions for these crimes by U.S. attorneys, who along with FBI agents have jurisdiction on most reservations, has been a longstanding point of contention for tribes who say it amounts to a second-class system of justice that encourages lawbreaking. Prosecutors, however, say they turn down most reservation cases because of a lack of admissible evidence.

Brendan Johnson, the U.S. attorney for South Dakota, said the government in recent years has deployed extra prosecutors and FBI agents to tribal areas. And the Justice Department says it is seeking to make its decisions more transparent. Impatience on reservations is understandable, Johnson said.

“If I had the rates of crime in my community that they do, I’d be mad too,” he said.

But tribes say they are rarely told why reservation cases are not pursued by the government.

“One of the basic problems is that not only are they declining to prosecute cases, but we are not getting the reason or notification for the declination,” said Jerry Gardner, executive director of the Tribal Law and Policy Institute in West Hollywood, Calif., which works with tribes to develop justice programs.

“The federal system takes a long time to make a decision, and when it comes to something like a child sexual assault, the community gets the message that nothing is being done.”

Under federal law, tribal courts have the authority to prosecute tribal members for crimes committed on reservations but cannot sentence those convicted to more than three years in prison. As a result, tribes may seek federal prosecution because penalties are harsher.

Frustration has grown so acute that some tribal members have taken the unusual step of suing the government for declining prosecutions and for what they say is the related issue of sloppy police work.

Last month, a federal court in Montana allowed the family of Steven Bearcrane, 23, of the Crow Reservation, to move ahead with a lawsuit against an FBI agent who Bearcrane’s parents say conducted a flawed homicide investigation into their son’s death. The lawsuit also said the U.S. Attorneys Office has a practice of rejecting criminal cases “in which the victims of those crimes are Native Americans.”

The Justice Department said it has made headway in resolving conflicts with tribes, pointing to a directive to U.S. attorneys to work more closely with tribal leaders and to the Tribal Law and Order Act, approved by Congress in 2010, which sought to strengthen tribal law enforcement systems.

But Tao Etpison, former chief judge of the Tonto Apaches in Arizona, said federal prosecutors typically live, work and try cases hundreds of miles from Indian Country. And at times, according to federal data, the Justice Department declines to prosecute violent reservation crime because local U.S. attorneys have said they lack sufficient resources.

“These crimes are very serious for the reservation, but the prosecutors really don’t see it from a reservation perspective,” Etpison said.

Federal prosecutors in 2011 declined to file charges in 52 percent of cases involving the most serious crimes committed on Indian reservations, according to Justice Department data compiled by the Transactional Records Access Clearinghouse at Syracuse University, which uses the Freedom of Information Act to recover and examine federal data.

The government did not pursue rape charges on reservations 65 percent of the time last year and rejected 61 percent of cases involving charges of sexual abuse of children, the federal data showed. In contrast, the Justice Department declines 20 percent of drug-trafficking cases nationwide, according to figures compiled by the clearinghouse.

Once federal prosecutors do decline a case, they seldom hand over evidence to tribal courts, according to the Government Accountability Office. A GAO report last year also found that federal prosecutors habitually fail to tell tribes that they have declined cases until after the tribe’s statute of limitations has expired.

Federal prosecutors, however, say they seek to provide as much information as possible to tribes about cases they decline, though they are often limited because the cases may be reopened later.

Kerry Jacobson, an assistant U.S. attorney in Wyoming, said that tribal prosecutions while the federal government decides whether it will file charges would create more problems than they would solve.

“We can’t turn over our evidence while we are doing our investigation,” she said. “And I don’t want victims of sexual assault to have to testify twice.”

Much of the time, however, victims do not testify at all.

On the San Carlos Reservation in Arizona, Etpison, the former tribal judge, said federal prosecutors had declined to pursue at least 40 sexual-assault cases in recent years, most of them involving children.

Thomas Weissmuller, a former chief judge for several tribes, said the problem hit home when he was on the bench 10 years ago on the Swinomish Reservation in Washington state.

Weissmuller said he presided over a trial in which a 31-year-old man was accused of pouring root beer schnapps into the root beer of a girl who had recently turned 13. The girl, unaware of the alcohol, drank the soda and passed out. The man covered her face with her own clothes and raped her.

Weissmuller said that despite a DNA match and statements from two family members who interrupted the attack, federal prosecutors declined to file charges or to provide the tribe with an explanation.

Although the man was convicted of rape in tribal court, he served only one year in jail — the maximum penalty allowed in the tribal judicial system at the time.

“I don’t know why it wasn’t prosecuted federally,” Weissmuller said. “I believe it was a very clear-cut case.”

The federal government declined to discuss details about the case.