It applies only to sexual assault crimes, and then only when prosecution is declined.
Drug-facilitated rape is one of the most commonly reported sexual assault crimes, Justice Department data show.
She said: "Here's the issue with domestic abuse, sexual assault, crimes that are intimate.
"No allied country changed its system in response to sexual assault crimes specifically or the rights of victims generally," General Gross wrote.
But others said they believed that removing the commander from the prosecution would help increase the amount of widely underreported sexual assault crimes by victims who fear retaliation.
Currently sexual assault crimes carry a maximum punishment of two years, but most convicted criminals can walk away by paying a small fee.
Ms. Gillibrand's proposal would have given independent military prosecutors, rather than commanders, the power to decide which sexual assault crimes to try, fixing a basic structural flaw in the military justice system that deters people from reporting assaults.
After a two-week investigation, the chief of the district attorney's sex crimes unit, Martha Bashford, wrote a letter to Mr. Kelly's lawyer saying "the facts established during our investigation do not fit the definition of sexual assault crimes".
The issue has become front and center on Capitol Hill, where Senator Kirsten E. Gillibrand, Democrat of New York, has sponsored a bill that would give independent military prosecutors, rather than commanders, the power to decide which sexual assault crimes to try.
