AN INVESTIGATION by the Air Force into sexual misconduct at its basic-training operations has identified 31 women who have been victimized. Just as troubling is that only one of the women came forward to report the abuse, a startling fact that reflects the pervasive mistrust in the military’s handling of sex crimes within its ranks. It has been two decades since the Tailhook scandal first focused attention on this issue; it’s clear that much more must be done to fix a system that has allowed the mistreatment of women who serve their country.

The widening scandal at Lackland Air Force Base in Texas, one of the country’s busiest military training centers, centers on allegations that male instructors assaulted, harassed and had sex with — in one case, raped — female trainees. Of all the military branches, the Air Force had been seen as the most accommodating to women. The allegations, distressingly similar to the 1996 abuse of female recruits and trainees at Aberdeen Proving Ground in Maryland, come as a powerful documentary, “The Invisible War,” depicts an epidemic of rape within the U.S. military.

“When does this ever end?” retired Air Force Brig. Gen. Wilma L. Vaught asks as the film details how a female soldier in combat zones is more likely to be raped by a fellow soldier than killed by enemy fire. The Defense Department estimated that 19,000 cases of sexual assault occurred last year, 3,200 of which were reported or investigated by the armed services. It’s hard to watch the film and not wonder why — despite years of Pentagon studies, congressional hearings, stern talk of “zero tolerance” and task-force recommendations — there hasn’t been more progress.

A major factor is how the system for prosecuting sex crimes has worked against the interests of victims. Decisions about whether a criminal case would go to trial were made by the immediate commander in the accused service member’s chain of command. Defense Secretary Leon E. Panetta, reportedly after watching “The Invisible War,” announced a policy change that requires the disposition of serious sex crime cases to be addressed by senior officers, at a minimum a colonel or Navy captain. Mr. Panetta had earlier begun initiatives to strengthen how the department prevents and responds to sexual assaults, including new support for victims.

Critics say that the changes don’t go far enough, and some are pressing for an overhaul of the military’s judicial system that would take decisions out of the chain of command and establish civilian supervision. It’s a move strenuously opposed by the military, which views the chain of command as the foundation for the order and discipline so vital to its mission. The new policy involving more senior and experienced officers, which went into effect only last week, must be given a chance, but if it fails to produce real results, the Pentagon must not hesitate to make additional changes. Among ideas with merit are empowering military prosecutors to make the final decision on cases or providing a process for victims to appeal decisions not to prosecute.

One area that clearly demands immediate attention is how the military punishes those who are accused or convicted of sex crimes. Analysis by the Service Women’s Action Network of 2011 Defense Department statistics showed that 10 percent of accused sex offenders were never held accountable because they were allowed to resign. Even more startling is its finding that one in every three convicted sex offenders was allowed to remain in the service. So much for zero tolerance.