Patrick Smith / Getty Images file The Navy-Marines Memorial Stadium in Annapolis, Md, is pictured in 2012.

Three U.S. Naval Academy football players are under investigation for alleged sexual assault last year against a female midshipman, sources have confirmed to NBC News.

It's alleged that the victim and the three students had been drinking when she reportedly had sex with one of them, her boyfriend, in the back seat of a car, sources said. The other two then allegedly had sex with the woman.

One was a senior set to graduate last week; his graduation was put on hold pending the investigation. The other two are juniors at the Annapolis, Md., school.

The sources said the victim initially reported the incident in February 2012 and the Naval Criminal Investigative Service immediately launched an investigation. Four months later, the woman essentially withdrew her complaint when she stopped cooperating with investigators, and the investigation was halted.

This past February, the woman renewed her complaint and the investigation was restarted.

No charges have been filed. The investigation is ongoing.

In 2007, the Academy expelled Navy quarterback Lamar Owens, Jr. in a sexual assault case. Although he was acquitted of any sexual assault, he was found guilty of conduct unbecoming an officer.

The problem of sexual assault in the military has been getting increasing attention, and data released recently shows that reported assaults are on the rise.

In fiscal year 2012, the number of reported assaults increased 6 percent to 3,374 — up from 3,192 from fiscal year 2011 – and the number of people who made an anonymous claim that they were sexually assaulted rose from 19,000 to 26,000, according to an annual Pentagon report released earlier this month.

The military's sexual assault-prevention unit has been in the news this month because of several high-profile cases involving abuse prevention officers.

On May 6, the Air Force officer in charge of that service's sexual assault program, Lt. Col. Jeff Krusinski, was arrested in an Arlington, Va., parking lot for allegedly groping a woman. He was charged with sexual battery and removed from his position pending an investigation.

On May 14, the Pentagon said an Army sergeant first class, assigned to III Corps at Fort Hood, Texas, was under investigation for allegedly forcing at least one subordinate into prostitution, abusive sexual contact, assault and maltreatment of subordinates. He has been suspended from his duties pending an investigation.

And on May 16, the head of the Army's equal opportunity and sexual assault-prevention office at Fort Campbell, Ky., was relieved of his duties over a dispute with his estranged wife. He was arrested by civilian authorities for violating a protective order sought by his wife, according to the Pentagon, and released on a $15,000 bond.

Last Friday, in a speech to the class of 2013 at the U.S. Naval Academy, Obama urged the 1,047 graduates to "live with integrity" and help restore trust in the military.

“Those who commit sexual assault are not only committing a crime, they threaten the trust and discipline that make our military strong,” he said.

NBC News' Courtney Kube, Tom Curry, and Elizabeth Chuck contributed to this report.