A female Air Force general has run afoul of Congress for granting clemency to a convicted sex offender without any public explanation, the latest case to raise fundamental questions about how the military justice system handles sex crimes.

The case is the second this year in which a three-star Air Force general has raised lawmakers’ hackles by effectively pardoning an officer found guilty of sexual assault. The twist this time, however, is that the general is a woman — a former astronaut who has served as a role model for other female officers as she climbed into the upper ranks of the Air Force.

Lt. Gen. Susan Helms, who as a crew member of the space shuttle Endeavour became the first U.S. military woman to travel in space in 1993, was poised to make another ascent in her career in March when the White House nominated her to become vice commander of the Air Force’s Space Command.

Since then, however, her nomination has been placed on hold by a member of the Senate Armed Services Committee who wants to examine her previously unpublicized decision to overturn an aggravated sexual-assault conviction for a captain at Vandenberg Air Force Base in California.

Helms’ action mirrors another case that has drawn angry attention from Congress and prompted legislators to propose landmark changes in military law. In that instance, victims’ advocates have called for the firing of Lt. Gen. Craig Franklin, the commander of the Third Air Force in Europe, after he tossed out the sexual-assault conviction of a star fighter pilot in February.

In both cases, the generals ignored the recommendations of their legal advisers and overruled a jury’s findings — without revealing why. Neither general was a judge and neither observed the trials, but intervened to grant clemency before the convictions could be heard by an appeals court.

Drew Pusateri, a spokesman for Sen. Claire McCaskill, D-Mo., said the lawmaker is blocking Helms’ nomination until she can receive more information about the general’s decision.

“As the senator works to change the military justice system to better protect survivors of sexual assault and hold perpetrators accountable, she wants to ensure that cases in which commanders overturned jury verdicts … are given the appropriate scrutiny,” Pusateri said.

The Pentagon has acknowledged that sexual assault in the military is widespread. It estimates that 19,000 offenses are committed each year, but that fewer than one in six cases are officially reported. Many victims have said they are reluctant to press charges because they lack faith in the military justice system. Of cases that are reported, only about one in 10 proceed to trial.

It is rare for commanders to grant clemency. The Air Force said it has recorded 327 convictions over the past five years for sexual assault, rape and similar crimes, but only five of those verdicts have been overturned in clemencies.

Advocacy groups, however, said any decision to overrule a jury’s verdict for no apparent reason has a powerful dampening effect.