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Mr. Hagel's decision to intervene comes amid mounting criticism from Congress as well as outside advocacy groups of the Pentagon's handling of a series of high-profile sexual assault cases in the military. In particular, critics have complained about the power of commanders to unilaterally dismiss criminal charges or convictions without explanation, which they say makes it less likely that women in the military will report sexual assaults for fear of retaliation.

Mr. Hagel said he would review the decision by Lt. Gen. Craig A. Franklin, the commander of the Third Air Force, to dismiss the sexual assault conviction of Lt. Col. James Wilkerson, a pilot who was also the inspector general of the 31st Fighter Wing at Aviano Air Base in Italy. Colonel Wilkerson was found guilty in November of aggravated sexual assault and was sentenced to one year in military prison. General Franklin's decision to overturn the findings of the court-martial freed Colonel Wilkerson, and allowed him to be reinstated in the Air Force.

In a March 7 letter to Senator Barbara Boxer, a California Democrat, and Senator Jeanne Shaheen, a New Hampshire Democrat, Mr. Hagel said that while General Franklin's decision could not be overturned, he had asked Pentagon lawyers and the secretary of the Air Force to review the way in which General Franklin decided the case. He also said he wanted a review of whether the military should change the way it handles sexual assault cases.

The furor over Colonel Wilkerson's case comes as the issue of sexual assaults in the military has been gaining prominence because of a recent string of scandals. The most wide-ranging case involves the Air Force's basic training program at Lackland Air Force Base in Texas, where 62 trainees were the victims of assault or other inappropriate actions by their instructors between 2009 and 2012. So far, 32 training instructors at Lackland have been charged, convicted or investigated in connection with the scandal.

On Wednesday, a Senate Armed Services subcommittee plans to hold a hearing on sexual assaults in the military, the first Senate hearing on the issue in nearly a decade, and Colonel Wilkerson's case is expected to be one of the focuses of the hearing.

The Wilkerson case has gained attention because it highlights what critics say is one of the biggest problems in how the military justice system handles sexual assault cases. In the system, senior commanders decide whether criminal charges are brought against military personnel, and even after charges are brought, the commanders also have the ability to veto the findings of a court-martial. That means the military justice system lacks the independence of the civilian law enforcement and judicial systems. For women who have been sexually assaulted, it means that their bosses decide whether charges are brought against their assailants, and that information about their assaults is shared in their workplaces.

Several women in the military have complained about the commanders' control of the legal process. Last year, the secretary of defense, Leon E. Panetta, said that while there were 3,191 reported cases of sexual assault in the military in 2011, the actual number of incidents was believed to be as high as 19,000, because most women do not report the assaults.

General Franklin's decision to overturn Colonel Wilkerson's conviction by a jury came after Colonel Wilkerson had failed a polygraph examination concerning the offenses, according to several people close to the case. General Franklin did not check with the victim before making his decision to dismiss the case, for which he has not given a detailed public explanation, and instead tried to promote Colonel Wilkerson and give him a new command, according to people familiar with the case.

General Franklin "was looking for a way to show the pilot community he had their backs," said one person familiar with the case.

Documents obtained in connection with Colonel Wilkerson's case also provide a glimpse into the fighter pilot culture of the Air Force that some women say encourages misogynistic behavior. In a personal e-mail he wrote while he was at Aviano in November 2011, Colonel Wilkerson, who had recently been named the inspector general of the Air Force's 31st Fighter Wing, describes his own behavior in a confrontation with military police. The e-mail, filled with bravado, expletives and fighter pilot jargon, describes an incident in which Colonel Wilkerson and other fighter pilots burned a couch in the middle of the base and then barked at the police and pulled rank to get them to back down when they came to investigate.

He wrote to another pilot that he deserved an award for helping ensure "the ability for the bros to either continue their merriment or skip away without notice." He added that he cared "about bros and traditions," and that he wanted to be remembered by his fellow pilots as someone who is "willing to stand up to the man, flip him the most wary of middle fingers, and then daring him to touch it."

The couch-burning incident was a small matter, but Colonel Wilkerson's belligerent treatment of the military security personnel who responded to the fire was considered more serious. The day after the incident, Colonel Wilkerson was dressed down by his commander, and the incident came back to haunt him during his trial, according to a person close to the case. After he attempted to provide evidence about his good military character, prosecutors were able to enter evidence about other incidents, including the couch-burning matter. Colonel Wilkerson's attorney, Frank Spinner, did not respond to a request for comment.