Allegations that not enough is being done to help victims or prosecute offenders have been raised from the service academies to the battlefields of Iraq and Afghanistan -- where hundreds of cases of sexual assault have been reported by women in uniform.
It was that revelation, plus pressure from Congress, that's forced the Pentagon to once again examine sexual misconduct in the military – which has been done 18 times in the last 16 years. The result has been more recommendations and sweeping policy changes.
But there are plenty of skeptics, and one of them is Lt. Jennifer Dyer, who talks to Correspondent Steve Kroft in her first interview after accusing a fellow officer of rape.
"They've done nothing but lie to me and treat me like a criminal," says Dyer.
Secretary of Defense Donald Rumsfeld says that he will have zero tolerance when it comes to sexual assault in the military.
To that, Dyer says, "I don't believe it. Zero tolerance would mean that I would not have been treated the way I've been treated."
When 60 Minutes first met Dyer, the Army was treating her like a criminal, threatening to arrest her for desertion. The eight-year veteran of the New Jersey National Guard had been AWOL for two months after refusing to return to Camp Shelby, Miss., where she says she was sexually assaulted by another lieutenant after a night of drinking with friends at the Officers Club.
"He raped you," asks Kroft.
"Yes," says Dyer.
"Is there any way he could have misinterpreted your intentions?" asks Kroft.
"I don't feel it's possible to misinterpret, 'No, don't do this. Or stop.' Those are the words that I used again and again," says Dyer.
Dyer says she reported the rape "within 10 to 15 minutes," and after she was taken to the emergency room to be examined, she was then sequestered for three days without access to a telephone.
She says her story was greeted with disbelief by military investigators and indifference from her command, which gave her only a two-week convalescent leave, then refused to extend it.
"They stated that two weeks was enough time to recover from such an incident," says Dyer. "I was told that if I didn't return on time, they would send MPs to my door and have me arrested."
Dyer, who was a law enforcement officer in civilian life, says she was willing to risk criminal charges rather than return to the place where her alleged assailant was still walking around.
She says she didn't want to return to Camp Shelby because she "was fearful for my health and safety and sanity."
All this happened just a few months after a Pentagon Task Force found that some commands showed "insensitivity" to rape victims and failed to appreciate "the need for long-term supportive care."
"The military as a whole has wished this issue would go away," says Scott Berkowitz, founder and president of the Rape, Abuse and Incest National Network – which runs the largest rape hotline in the country. He also worked with the Pentagon task force on sexual assault, a crime he believes is much more prevalent in the military than in civilian life.
"Three out of every 100 military women say that they were sexually assaulted. That compares to – the equivalent civilian rate for women that age – it's about 3 in a thousand," says Berkowitz. "So if the defense department numbers are right, the problem in the military could be as much as 10 times the civilian problem."
Part of the problem has to do with relatively small numbers of women living and working with much larger numbers of men, often far from home and family. It is a young population and alcohol is a factor in 70 percent of the cases, which usually involve people who are at least acquainted with each other.
Often, the cases are hard to prove. And in a military culture still dominated by men, the decision on whether or not to prosecute almost always rests with the male commander.
Berkowitz says that the chances of actually going to prison, if you're accused of rape in the military, is "pretty slim."
What does Berkowitz think is the biggest problem with the way the military has been handling rape cases?
"I think the crux of the problem is confidentiality," says Berkowitz. "The fact that immediately everyone you know will know what happened to you is a huge disincentive to come forward."
"Before I returned from the hospital the next morning, I found out that my entire command had been told in formation by the company commander what had happened," says Lance Cpl. Sally Griffiths.
What happened to Griffiths and other female veterans that Kroft talked to are typical of the complaints leveled against the military for more than a decade.
"There's a survey that found that 30 percent of female veterans said that they had either been victims of rape or attempted rape. Do you think the problem is that prevalent," asks Kroft.
The group responded: "Definitely. Absolutely, if not more."
"I think when they see what happens, they fear the retribution," says Griffiths.
Griffiths was stationed on Okinawa in 1993 when she reported she was raped by a fellow Marine, yet she was the one accused of making false statements. As the investigation unfolded, she happened to stumble across her own case file.
It included a polygraph statement in which the suspect "...admitted that victim had made the statement, 'But, I don't want to,' prior to ... penetration..."
"I noticed a filing cabinet with my name on it and the case files. And I began to look through there because they had accused me of lying," says Griffiths. "And I found in the case file that the suspect had confessed. I made photocopies, sent it home to my parents, who took it to a local senator -- at which point, he was instrumental in helping me get out of the military."
What happened to the soldier? "Nothing," says Griffiths. "He served six more years and was promoted several times."
Sharon Mixon was a staff sergeant, and a highly decorated combat medic during Operation Desert Storm. She was in Saudi Arabia, and about to come home, when she says she was drugged and gang-raped.
"I woke up face down on a cot. I was being held down. And there were six men taking turns raping me," recalls Mixon. "They were U.S. soldiers, and they told me that if I told anybody that they would kill me. But I went and told the MPs anyway. And they told me the same thing."
"They kind of laughed and said, 'Well, what did you expect, being a female in combat? And we will always know where to find you. And if you open your mouth, you know what's gonna happen,'" adds Mixon, who kept quiet for more than 10 years.
Mixon continued her military career until she said she began having flashbacks and was hospitalized for post-traumatic stress disorder. She has actively lobbied Congress on behalf of military rape victims.
"I had been awarded for valor in combat," says Mixon. "I went from being a standard-setting soldier to being something that they wanted to hide in a closet."
"They want to brush it under a rug. They want it to go away," says Marine Lt. Tara Burkhart, who comes from a military family. She was serving with distinction as a public affairs officer in Kuwait during Operation Iraqi Freedom, escorting reporters in and out of the combat zone. She and several enlisted men from her unit were invited to a party thrown by Kuwaiti nationals to thank them for all they had done.
"During the course of that evening, the sergeant who was under my command raped me," says Burkhart, who didn't initially report it. "I was afraid. I had seen what other people had gone through when they had tried to report sexual assault or rape."
She didn't say anything, until allegations surfaced that she and her men had violated orders by drinking at the party, and that she had sex with a subordinate.
"I got my attorney. And he immediately contacted the command," says Burkhart. "'This is crazy, my client was raped.' And my command said, 'No, she's lying. We don't believe her. You shouldn't either. And we're gonna prosecute her. She's gonna go to a court-martial.'"
Lt. Burkhart was charged with 19 counts, including sexual misconduct, providing alcohol to enlisted men, making false statements and disobeying orders – charges that could have sent her to prison for 26 years.
The soldier who Burkhart says raped her was later accused in another rape. "He was accused during my investigation," says Burkhart. "The other victim came out and claimed that he raped her in Kuwait, too."
Burkhart says the soldier was never prosecuted: "There has never been any charges brought against him. He was given a grant immunity to testify against me."
Burkhart was eventually acquitted of the most serious charges, including sexual misconduct, but served 30 days for violating alcohol policies and disobeying orders.
As for her career, Burkhart says, "It's over. It's over."
"I think most of these women will tell you, 'The rape was bad enough. How the military treated me was worse,'" says Rep. Loretta Sanchez of California. She is the ranking female on the House Armed Services Committee, and one of the strongest Congressional advocates for military victims of sexual assault.
"If you talk to a lot of them, they'll tell you, 'I'm the one that was, you know, drummed out of the military. I'm the one that suffered from this. All they did was move him to a different unit. He's still out there.' In case after case."
Sanchez tried unsuccessfully to get the Pentagon to update what she calls "archaic" military statutes on sexual assault that were written more than 50 years ago. She says they need to be brought in line with current civilian laws and changing attitudes.
"We have a society that's very tough on the victim," says Sanchez. "And in the military, it's even worse because some commanding officers say, 'You know, you should be tough enough to take it. You know, I don't want you impacting the morale of my unit by accusing someone of being a rapist. Can't you be one of the boys?'"
But Sanchez, who was a rape victim herself while she was in college, is not giving up: "They want it to go away. They want me to go away. They want the subject to go away. It's not going to go away."
The Pentagon declined a request from 60 Minutes for an interview. But last month, under pressure from Congress, Undersecretary of Defense David Chu announced sweeping policy changes recommended by the Pentagon Task Force.
"The department understands that our traditional system does not afford sexual assault victims the care and support they need across the board," says Chu. "And we are moving aggressively to put new systems in place to address this shortcoming."
The changes include mandatory education on sexual assault for everyone in the armed services, the designation of a victim advocate for every military command, the promise of confidentiality for rape victims until a formal investigation begins, and the appointment of Brig. Gen. KC McClain to oversee the entire process.
"This is not a silver bullet. There is no overnight solution," says McClain. "And to do this right, it is going to take time."
Berkowitz wants to believe it's progress.
"There was a task force the year before that came out with some great recommendations. Which is good. The problem is, there was a task force before that and there were 10 task forces before that," says Berkowitz.
"And every time, as soon as the public interest and the media attention died down, the reports of the task force were quickly filed and forgotten. The good news is that this time they seem a lot more serious about fixing the problem."
This time, Congress is demanding more than promises. It wants to see the Pentagon's plan for implementing the new policies and proposed changes to military law within the next two weeks.
The glare of publicity may have already affected one case. Shortly after 60 Minutes interviewed Lt. Dyer, the Army dropped its threat to prosecute her for desertion and granted her request for an honorable discharge.
The officer she accused of assaulting her is now being court-martialed for rape. He maintains the sex was consensual.