Only 240 cases of sexual assault in the military were prosecuted in 2011, out of more than 3,000 reported cases. The Department of Defense estimates that the number of actual sexual assaults in the military each year is closer to 19,000, although many service members never come forward out of fear of retaliation.
Panetta said he is making it a priority this year to crack down on military rape cases.
"These are tough cases, but the fact is, we can do this," he said in the interview, which airs Thursday night on NBC's "Rock Center with Brian Williams." "We need to improve the investigations and ensure we have prosecutors that are willing to take these cases to court."
While the military has been accused of ignoring rape cases for years, the recent sexual assault scandal at the Lackland Airforce Base in Texas has focused national attention on the problem. Six basic training instructors at Lackland were charged with sexual misconduct involving at least 43 women, but the punishments for some of the perpetrators so far have been mild. After one of the instructors, Jason Manko, confessed to having had a sexual relationship with a trainee, he was sentenced to only 45 days in jail and was allowed to remain in the military.
Panetta said he doesn't think the Lackland scandal is an isolated problem.
"What we learned from what happened at Lackland Air Force Base is that there's a power game that can go on here that I think reflects what's happening in society in general," Panetta said. "When you've got 19,000 sexual assaults taking place, this is something that's happening elsewhere as well."
As part of her report on the military's handling of sexual assault cases, Morales interviewed several women in the military who reported having been raped. Four of the women she interviewed all said that their assailants had served no prison time and that they faced retaliation after reporting the crime.
Darchelle Mitchell, one of the rape survivors that Morales' segment will feature, says that her colleague was not found guilty of raping her despite DNA evidence linking him to the rape. Instead, she was kicked out of the military for reporting it.
Asked what he would tell these victims, Panetta said, "I guess I want them to know that as difficult as their experience has been, that we're going to learn from that."