A Defense Department directive last week about sexual assault in the military went largely unnoticed and unreported, but it’s important. It puts military leaders’ feet to the fire in addressing what Defense Secretary Leon Panetta rightly calls an “outrage” and a “silent epidemic.”

One rape that goes unpunished in the U.S. military would be wrong. But in our military, there are thousands. There were nearly 3,200 reported cases of sexual assault in the military last year, but a Pentagon survey shows the actual number was close to 19,000 because most aren’t reported.

That’s unconscionable. As unconscionable is why so many of these crimes go unreported and unpunished.

One reason is obvious. Perpetrators are sometimes supervisors of their victims. That’s what happened in a recent high-profile case involving Lackland Air Force Base. One instructor has been convicted of rape and multiple cases of sexual assault of female trainees, and 16 other trainers have been charged or are under investigations for crimes ranging from aggravated sexual assault to improper sexual relationships with 42 female trainees.

The Lackland case joins several other notorious cases including the Navy’s Tailhook convention in Las Vegas in 1991 that involved 83 female and seven male victims of sexual assault by more than 100 Navy and Marine Corps aviation officers, the Army’s Aberdeen Proving Ground in 1996 where 12 Army officers were charged with sexually assaulting female trainees, and the Air Force Academy in 2003 where 12 percent of female graduates reported having been victims of rape or attempted rape, and 70 percent said they had been sexually harassed. Closer to home, a hearing officer was appointed this week to probe sexual assault charges against an Army general from Fort Bragg.

A recent film, “The Invisible War,” has spotlighted sexual assault in the Marines. It reportedly prodded Panetta to change military policy on how rape charges are investigated and prosecuted. The decision is now in the hands of senior commanders, not lower level officers. The documentary includes interviews with five female Marines who reported having been raped. But the Corps instead investigated and disciplined four of the women – not their alleged perpetrators. None of the accused officers was punished.

That has been a pattern in too many cases, observers say. The alleged victims and not the alleged perpetrators become the subject of scrutiny. That’s because sexual assault charges are often treated as a disruption in the orderly operation of the service and not as crimes, some say.

None of that makes it easy or advantageous for victims to step forward.

Panetta said that’s wrong: “Any sexual assault has no place in the military…. If we don’t take steps to deal with it – if we don’t exercise better leadership to confront it – it’ll get worse… I have men and women in the military who put their lives on the line … to protect this country. Surely we owe it to them to be able to protect them.”

The defense secretary has ordered all services to improve the quality of sexual assault prevention training for their prospective commanders and senior enlisted leaders. Ways to reduce the frequency of sexual assaults must be identified and reported back to Panetta by next February.

Punishing offenders is also important, Panetta said. “It’s an outrage that we aren’t prosecuting our people involved,” he said when told that just 240 cases were prosecuted out of the more than 3,000 reported last year. Military leaders must take responsibility for addressing that issue, he said. Special victims units are being put in place to improve investigations.

These are welcome moves, though they come too late for thousands of women and men who’ve already suffered. But they’re not too late for others. Sexual assaults are crimes. It’s past time that the U.S. military established zero tolerance for them.