WHETHER THE right decisions were rendered last week in the military’s two high-profile cases of sexual assault is a matter of some dispute. Given the shape of the cases before them, we tend to think the judges in both probably made the right calls. But the process along the way was so flawed that it’s hard to have any confidence that justice was done.

The cases have renewed attention on the need to change a military justice system that is susceptible to letting factors other than the evidence influence which sexual assault cases are brought to trial. One involved Brig. Gen. Jeffrey A. Sinclair, reprimanded for mistreating an Army captain with whom he had an affair; the other, Midshipman Joshua Tate, a former Naval Academy football player acquitted of sexual assault. Both show why trained, independent prosecutors, not commanding officers with competing concerns, should be in charge of deciding which cases come to trial. Legislation championed by Sen. Kirsten Gillibrand (D-N.Y.) that would have brought about this critical reform got 55 votes in the Senate this month, a clear majority but unfortunately five short of the 60 needed to overcome a filibuster.

Most of the debate on removing decisions about whether to prosecute sexual assault cases from the chain of command has focused on the understandable concerns that conflicts of interest by commanding officers make it difficult for victims to get a fair hearing. The cases of Gen. Sinclair and Mr. Tate present the flip side of the argument. In both instances, commanding officers ignored warnings from military lawyers about weaknesses in the cases and insisted on going to trial, apparently to show the military’s new seriousness in not tolerating sexual misconduct. No doubt there was heightened political pressure with Congress considering Ms. Gillibrand’s controversial legislation and the Senate putting a hold on Air Force Lt. Gen. Susan Helms’s nomination as vice commander of the U.S. Space Command because she overturned a jury conviction in a sexual assault case.

It is telling that attorneys for both the defense and the accuser in the Naval Academy case told the New York Times they see the system as broken. Clearly the superintendent of the Naval Academy erred in going to trial with a bad case, but one wonders what how much of that was because of the botched NCIS investigation. The case was also marked by the appalling hours of abusive pre-trial questioning to which the woman was subjected, an issue that thankfully was addressed with reforms to the Uniform Code of Military Justice enacted last year.

No one, as Ms. Gillibrand argued in support of her legislation, wants to see an innocent soldier going to jail or a guilty perpetrator going free. Sexual assault cases — be they in the military or civilian world — are often difficult to investigate and try. Lack of public confidence in how justice is dispensed compounds the problem, making victims fearful to come forward and others reluctant to cooperate. Congress needs to revisit this issue.