TOKYO >> After a night of heavy drinking at the Globe and Anchor, a watering hole for enlisted Marines in Okinawa, Japan, a female service member awoke in her barracks room as a man was raping her, she reported. She tried repeatedly to push him off. But wavering in and out of consciousness, she couldn’t fight back.

A rape investigation, backed up by DNA evidence, ended with the accused pleading guilty to a lesser charge, wrongfully engaging in sexual activity in the barracks. He was reduced in rank and confined to his base for 30 days, but received no prison time.

Fast forward a year. An intoxicated service member was helped into bed by a male Marine with whom he had spent the day. The Marine then performed oral sex on the victim "for approximately 20 minutes against his will," records show. The accused insisted the sex was consensual, but he was court-martialed, sentenced to six years in prison, busted to E-1, the military’s lowest rank, and dishonorably discharged.

The two cases, both adjudicated by the 1st Marine Aircraft Wing, are among more than 1,000 reports of sex crimes involving U.S. military personnel based in Japan between 2005 and early 2013. Obtained through the Freedom of Information Act, the records open a rare window into the world of military justice and show a pattern of random and inconsistent judgments.

The Associated Press originally sought the records for U.S. military personnel stationed in Japan after attacks against Japanese women raised political tensions there. They might now give weight to members of Congress who want to strip senior officers of their authority to decide whether serious crimes, including sexual assault cases, go to trial.

The AP analysis found the handling of allegations verged on the chaotic, with seemingly strong cases often reduced to lesser charges. In two rape cases, commanders overruled recommendations to court-martial and dropped the charges instead.

Even when military authorities agreed a crime had been committed, the suspect was unlikely to serve time.

Nearly two-thirds of 244 service members whose punishments were detailed in the records were not incarcerated. Instead they were fined, demoted, restricted to their bases or removed from the military. In more than 30 cases, a letter of reprimand was the only punishment.

Among the other findings:

–The Marines were far more likely than other branches to send offenders to prison, with 53 prison sentences out of 270 cases. By contrast, of the Navy’s 203 cases, more than 70 were court-martialed or punished in some way. Only 15 were sentenced to time behind bars.

–The Air Force was the most lenient. Of 124 sex crimes, the only punishment for 21 offenders was a letter of reprimand.

–Victims increasingly declined to cooperate with investigators or recanted, a sign they may have been losing confidence in the system. In 2006, the Naval Criminal Investigative Service, which handles the Navy and Marine Corps, reported 13 such cases; in 2012, it was 28.

Taken together, the sex crime cases from Japan, home to the largest number of U.S. military personnel based overseas, illustrate how far military leaders have to go to reverse a spiraling number of sexual assault reports.

In one case, a woman alleged that a sailor raped her. Later, she confronted him in a recorded conversation. She accused him of pushing her down "for sex purposes," after which he apologized for hurting her "in that way."

An Article 32 hearing, the military’s version of a grand jury, recommended a court-martial on rape charges, but the commanding officer said no. The charges were dropped.

U.S. Sen. Kirsten Gillibrand, who leads the Senate Armed Services’ personnel subcommittee, said the records are "disturbing evidence" that there are commanders who refuse to prosecute sexual assault cases.

The AP story "shows the direct evidence of the stories we hear every day," said Gillibrand, who leads a group of lawmakers from both political parties pressing for further changes in the military’s legal system.

"The men and women of our military deserve better," said Gillibrand, D-N.Y. "They deserve to have unbiased, trained military prosecutors reviewing their cases, and making decisions based solely on the merits of the evidence in a transparent way."

Air Force Col. Alan Metzler said the Department of Defense has been open in acknowledging that it has a problem.

"We have owned that," he said. "We have been public about it."

Metzler, deputy director of the Defense Department’s Sexual Assault Prevention and Response Office, said the changes in military law and policy made by Congress and the Pentagon are creating a culture where victims trust that their allegations will be taken seriously and perpetrators will be punished. The cases in Japan preceded reforms the Pentagon implemented in May, according to defense officials.

The military, Metzler noted, is making progress. The number of sexual assault cases taken to courts-martial military-wide has grown steadily, from 42 percent in 2009 to 68 percent in 2012, according to department figures. In 2012, of the 238 service members convicted, 74 percent served time.

That trend is not reflected in the Japan cases. Out of 473 sexual assault allegations against sailors and Marines between 2005 and 2013, just 116, or 24 percent, ended up in courts-martial.

Further, the 238 convictions are a small number compared with the estimated 26,000 sex crimes that may have occurred that year across the military, according to the department’s anonymous survey of military personnel. Sex crimes are vastly underreported in both military and civilian life.

The top U.S. officer in Japan, Lt. Gen. Salvatore Angelella, said the military takes the issue of sexual assault "very seriously."

"Sexual assault is a crime and a contradiction to everything we stand for," he said.

The NCIS provided more than 600 case files — seven years of detailed but heavily redacted executive summaries of sex-crime reports. The four military branches provided another 400 files covering narrower time frames.

The Pentagon has said its commanders have been using nonjudicial punishment less frequently in recent years. But the documents show that in Japan at least, U.S. commanders are using that authority more often. This is especially true in the Navy, where in 2012 only one case led to court-martial. In the 13 others, commanders used nonjudicial penalties rather than ordering trials.

The authority to decide how to prosecute serious criminal allegations would be taken away from senior officers under a bill crafted by Gillibrand and expected to come before the Senate as early as this coming week. The legislation would place that judgment with trial counsels who have prosecutorial experience and hold the rank of colonel or above.

Senior U.S. military leaders oppose the plan, saying it would undermine the ability of commanders to ensure discipline within their ranks.

"Taking the commander out of the loop never solved any problem," said U.S. Sen. Lindsey Graham of South Carolina, a former Air Force lawyer who is the personnel subcommittee’s top Republican. "It would dismantle the military justice system beyond sexual assaults. It would take commanders off the hook for their responsibility to fix this problem."

Graham, a member of the Air Force Reserves who is an instructor at the service’s judge advocate general school, said victims of sexual assault have a far better chance of getting justice than do victims whose cases are handled by civilian courts.

But research by Cassia Spohn, a professor of criminology and criminal justice at Arizona State University, found that civilian courts prosecute sexual assault cases at a higher rate than the military — 50 percent compared with 37 percent.

Spohn cautioned that comparing the two sectors is a dicey exercise.

State and local prosecutors typically only file charges in cases they have a solid chance of winning. Conversely, the military may be able to secure at least mild punishment, such as a reduction in rank or loss of pay, in a weaker case because they have more options to penalize.

The military leadership’s time to solve the crisis on its own has run out, according to Pentagon critics. A string of episodes in which senior officers were caught behaving badly is further proof that serious crimes should be dealt with outside the chain of command, they say.

"There is a perception out there right now that the military is out of control," said K. Denise Rucker Krepp, a former Coast Guard officer and attorney. "You are not going to attract the best and the brightest if people believe that if you go into the military you are going to be sexually assaulted."

Mark Russell, a psychologist and former Navy commander who was stationed in Japan, said putting commanders in charge of deciding how to proceed with sex abuse allegations can conflict with the unit’s mission.

"The mission trumps every other aspect of military life, including sometimes, legal justice and moral standing," wrote Russell, now a professor at Antioch University in Seattle, in an email. "A climate emerges, whereby individuals may feel they can act with impunity, especially in the case … where it may be ‘he said, she said,’ with ‘good workers’ often given the benefit of the doubt."

Many of the Japan cases involved an accuser who said he or she was sexually abused while too drunk to consent, or even unconscious. That makes it all the more difficult to determine whether a crime occurred.

"Weakness is a great fear in the military and something to be avoided," Russell wrote. "Therefore, women (or men) who go out drinking and are raped are often viewed as culpable for having been ‘weak and vulnerable.’"

The documents analyzed by the AP do not reveal whether certain commanders had a tendency to punish outside the courts-martial process. Names of the accusers, the accused and commanders are all deleted — for privacy, the military said.

When compared with broader statistics released annually by the Pentagon, the documents suggest that U.S. military personnel based in Japan are accused of sex crimes at roughly the same rate as their comrades around the world.

But bad behavior here by American sailors, Marines, airmen and soldiers can have intense repercussions in this conservative, insular country, an important U.S. ally. This is especially true on the island of Okinawa, home to barely 1 percent of Japan’s population but about half of the roughly 50,000 U.S. forces based in the country.

Sex crimes against Okinawans have become major news stories, and added fury to protests against the U.S. military’s presence on the island.

But the documents show that, as it is at U.S. bases everywhere, U.S. service members who commit sexual assaults are most likely to abuse their own comrades.

More than three dozen NCIS case summaries describe investigations that appeared to indicate a sex crime, but were resolved using lesser charges or simply dropped with little or no explanation.

Such is the case for an investigation that began in January 2008 against a Navy doctor who would go on to sexually abuse women in the military until his clinical privileges were suspended in 2009.

Airman Tina Wilson’s name is redacted from the report, but she spoke up a day after she went to the health clinic at Naval Air Facility Atsugi, a U.S. base southwest of Tokyo, to have a dressing changed following surgery on her tailbone.

In Wilson’s sworn statement to NCIS and other records, the doctor, Lt. Cmdr. Anthony L. Velasquez, walked over to look at the wound as a corpsman took care of the dressing. Then Velasquez announced that the results were in from a staph-infection test, and that he was going to check Wilson’s lymph nodes.

He checked her neck, then went under her shirt and ran his hands up the sides of her torso. Then he asked Wilson, whose pants were unzipped because of the dressing change, to lie on her side. He felt her left hip bone, then slid his hand down the front of her pants and under her panties.

Wilson pulled up her pants, and confused and shaken, headed for the door.

"I saw Dr. Velasquez smile and wink at me on the way out," her sworn statement reads. "He was by the computer getting hand sanitizer. The whole exam, he didn’t wear gloves."

The NCIS document summarizing the investigation prompted by Wilson’s complaint shows that three other women subsequently came forward, saying Velasquez had touched them inappropriately.

Nevertheless, after 10 months the investigation was closed with no action. According to the document, Yokosuka Naval Hospital declined to take any action against the doctor, and the Navy legal services office in Yokosuka determined the case would not be forwarded to Navy officials in San Diego who oversee medical operations in Japan.

Finally in 2010, after accusations from more than two dozen women, the Navy filed multiple counts of sexual misconduct and other charges against Velasquez.

Most of the charges were dropped under a plea deal. Velasquez served a week in the brig, was dismissed from the Navy, lost his license to practice medicine, and was required to register as a sex offender.

Retired Rear Adm. Richard B. Wren, the former commander of Navy forces in Japan who oversaw Velasquez’s court-martial, did not return telephone calls seeking comment.

Wilson, 27, left the Navy, distraught over how her case had been handled.

The U.S. military has come under fire even when it did not have legal jurisdiction in a sexual assault case.

Catherine Fisher, an Australian and longtime Japan resident, accused the Japanese and U.S. governments of "harboring the suspect" after she was raped, allegedly by an American sailor, in 2002.

Japanese prosecutors refused to pursue criminal charges for undisclosed reasons, but in 2004 the Tokyo District Court ruled in a civil case that Fisher had indeed been sexually assaulted, and awarded her 3 million yen ($30,000) in damages.

By then the accused, Bloke T. Deans, had left the country. Fisher and her attorneys said the Navy was aware of the Japanese court case against Deans, but gave him an honorable discharge and allowed him to leave the country without informing the court or her.

U.S. military officials refused to disclose his whereabouts, citing privacy reasons, she said. A spokesman for U.S. Forces Japan declined comment on Fisher’s case and said the command does not track the whereabouts of former service members.

Fisher tracked Deans down in Milwaukee, and sued in Wisconsin Circuit Court in 2012 to claim the damages awarded in Japan. Last year, she won, but settled for $1 — to make a point.

Deans denied he assaulted Fisher but acknowledged in the U.S. settlement "the evidence may prove otherwise," according to documents provided by his attorney, Alex Flynn. "Mr. Deans has paid that dollar and the matter is now concluded," Flynn said.

Not for Fisher, who became an advocate for rape victims in Japan. "Governments get out there and say, ‘We are against rape, and we are doing everything we can,’ but in fact they are not," she said. "And by not allowing rape victims to receive justice, it’s just going on in the same pattern."

After a long and contentious debate, Congress late last year passed numerous changes to the military’s legal system in an effort to combat the epidemic of sexual assaults.

The defense policy bill scaled back but did not eliminate the role senior commanders play in sexual assault cases. Officers who have the power to convene courts-martial were stripped of their authority to overturn guilty verdicts reached by juries, and should they decline to prosecute a case, a review of the decision must be conducted by the service’s civilian secretary.

The argument for keeping commanders involved in sexual assault cases received a boost from a panel of experts, which said last month that there is no evidence that removing commanders from the process will reduce sex crimes or increase the reporting of them.

"I don’t know how we can trust our commanders to train our sons and daughters to fight and win our nation’s war and yet not trust them to provide and establish a command climate that provides each and every soldier a safe working environment," said retired Gen. Ann Dunwoody, the Army’s first female four-star.

Gillibrand and her supporters argue that the cultural shift needed to lower the incidence of sexual assault in the military won’t happen if commanders retain their current role in the legal system.

"Skippers have had this authority since the days of John Paul Jones and sexual assaults still occur," said Lory Manning, a retired Navy captain and senior fellow at the Women in the Military Project. "And this is where we are."

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Lardner reported from Washington. Associated Press writer Leon Drouin-Keith in Bangkok, and AP researchers Monika Mathur in Washington and Rhonda Shafner in New York contributed to this report.

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Online:

Nearly 600 documents, obtained by the AP from the U.S. Naval Criminal Investigative Service through the Freedom of Information Act., of sexual assault cases involving U.S. military personnel at bases in Japan from 2005 to early 2013, are available at: http://hosted.ap.org/specials/interactives/_documents/military-sexual-assaults