Seventeen former and active-duty service members filed a class-action lawsuit this week against Defense Secretary Robert Gates and his predecessor, Donald Rumsfeld, alleging that the military had failed to stop rapes, investigate reported crimes or prosecute perpetrators. Despite ample evidence of the problem, the suit alleges, Gates and Rumsfeld “ran institutions in which perpetrators were promoted . . . and Plaintiffs and other victims were openly subjected to retaliation.” While the suit is new, the problem of sexual assault of service members by other service members has long been known to the military leadership.

The Defense Department recorded 3,230 sexual assaults involving members of our military in fiscal 2009, up 11 percent from 2008. But the Pentagon itself concluded in 2006 that only 20 percent of “unwanted sexual contacts” are reported to a military authority, about half of the rate in the civilian sector. Victims of military sexual assault are often forced to choose between frequent contact with the perpetrators or sacrificing their career goals to protect themselves from retaliation, the Department of Veterans Affairs notes.

If they do come forward, victims face military rules that are years behind standard law enforcement procedures for sexual assault. Forty percent of reported sexual assaults result in prosecution in civilian courts, according to the 2005 National Crime Victimization Study. But the analogous figure in the military is just 8 percent. Victims in the services are not guaranteed access to military lawyers, nor is the confidentiality of conversations with victims’ advocates guaranteed. If victims choose a “restricted” reporting route — one of two options — they are not allowed to discuss the trauma, including with friends, which increases the risk of post-traumatic stress disorder. But the details of the other reporting option mean victims’ superiors can often ascertain the identities of those who have come forward, increasing the risk of retaliation.

The Pentagon has taken steps to reduce the frequency of rape: It created the Sexual Assault Prevention and Response Office in 2005 with the goal of implementing prevention programs across the services. (A Government Accountability Office assessment of these efforts in 2008 suggested the military has only “limited visibility” over such incidents.) In 2009 it established a task force to study the issue and make recommendations.

But the military is still not making available accurate statistics about the extent of the problem or the services and benefits that survivors have received, so progress is difficult to measure. The Service Women’s Action Network and the ACLU filed suit in December, demanding that these data be released.

Sexual assault is associated with high rates of post-traumatic stress disorder in men and women and an even higher rate of PTSD than that reported by men after exposure to combat, according to the VA’s Iraq War Clinician Guide. Soldiers who experience sexual assault are also at higher risk of PTSD than civilians.

A 2006 study by Naomi Himmelfarb and colleagues at the West Los Angeles VA Healthcare Center found that 60 percent of women exposed to military sexual trauma developed PTSD. Soldiers are already under extraordinary stress, the reasoning suggests, and, in situations where loyalty to the unit is a matter of life and death, it is even more difficult to process or talk about the trauma. Compounding these procedural shortcomings are the constraints of military service: Unlike civilians, victims cannot quit their jobs without risk of imprisonment, so they may be repeatedly retraumatized by being in the presence of their abuser.

It is also significantly more difficult for victims of sexual assault to obtain benefits for PTSD than victims of other kinds of trauma. The VA eased rules last July regarding benefits for psychological injuries, but victims of military sexual trauma are often unable to provide sufficient proof of an “initial stressor” that caused their PTSD. Neither Congress nor the military has acted to remove bureaucratic hurdles hindering provision of PTSD benefits to rape victims.

The defense authorization bill President Obama signed into law last month includes a provision authored by Reps. Niki Tsongas (D-Mass.) and Mike Turner (R-Ohio) that would improve prevention and response policies. The House version of the bill required that all victims of sexual assault be guaranteed access to a lawyer, but the Senate required only that the Defense Department “study the feasibility of” providing a military lawyer to all victims of sexual assault.

At minimum, conversations with victim advocates need to be made confidential and immune from discovery if cases go to court, as they typically are when sexual assaults occur in the civilian sector.

Denying the significance of sexual crimes is not unique to the military. But in the case of military sexual assaults, the costs are especially far-reaching. Tacit tolerance of sexual assaults severely damages the morale and resilience of individual service members. It also threatens more than individuals: It undermines readiness and mobilization capacity and, ultimately, our national security.

Jessica Stern, the author of “Denial: A Memoir of Terror,” is a member of the Hoover Institution Task Force on National Security and Law.