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 episodes 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.