At US military bases in Japan, most service members found culpable in sex crimes in recent years did not go to prison, according to internal Department of Defence documents. Instead, in a review of hundreds of cases filed in America’s largest overseas military installation, offenders were fined, demoted, restricted to their bases or removed from the military.

In about 30 cases, a letter of reprimand was the only punishment.

More than 1,000 records, obtained by the Associated Press through the Freedom of Information Act, describe hundreds of cases in graphic detail, painting a disturbing picture of how senior American officers prosecute and punish troops accused of sex crimes. 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. Of 244 service members whose punishments were detailed in the records, only a third were incarcerated.

The analysis of the reported sex crimes, which were filed between 2005 and early 2013, shows a pattern of random and inconsistent judgments. The marines, for example, 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-martialled 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, the figure was 28.

In two cases, both adjudicated by the 1st Marine Aircraft Wing, the accusers said they were sexually abused after nights of heavy drinking, and both had some evidence to support their cases. One suspect was sentenced to six years in prison, but the other was confined to base for 30 days instead of getting jail time.

Taken together, the cases illustrate how far military leaders have to go to reverse a spiraling number of sexual assault reports. The records also may give weight to members of Congress pushing to strip senior officers of their authority to decide whether serious crimes, including sexual assault cases, go to trial.

“How many more rapes do we have to endure to wait and see what reforms are needed?” asked Senator Kirsten Gillibrand, chair of the Senate armed services personnel subcommittee. She leads a vocal group of lawmakers from both political parties who argue that further reforms to the military’s legal system are needed.

Air Force Colonel Alan Metzler, deputy director of the Defence Department’s sexual assault prevention and response office, said the department “has been very transparent that we do have a problem”. He said a number of changes in military law is creating a culture where victims trust that their allegations will be taken seriously and perpetrators will be punished.

The number of sexual assault cases taken to courts martial has grown steadily – from 42% in 2009 to 68% in 2012, according to DOD figures. In 2012, of the 238 service members convicted, 74% served time.

That trend is not reflected in the Japan cases. Out of 473 sexual assault allegations within navy and marine corps units, just 116, or 24%, ended up in courts martial. In the navy, one case in 2012 led to court martial, compared to 13 in which commanders used non-judicial penalties instead.

The authority to decide how to prosecute serious criminal allegations would be taken away from senior officers under a bill crafted by Gillibrand that is expected to come before the Senate this week. The bill would place that responsibility with the trial counsel who has prosecutorial experience. Senior US military leaders oppose the plan.

“Taking the commander out of the loop never solved any problem,” said Senator Lindsey Graham, 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.”

Gillibrand and her supporters argue that the cultural shift the military needs will not 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.”