An 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, a crime many experts see as a growing problem in the military.

This time the general is 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 J. 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.

But her nomination has been blocked by Sen. Claire McCaskill (D-Mo.), a member of the Armed Services Committee, who wants to examine Helms’s previously unpublicized decision to overturn the conviction, on charges of aggravated sexual assault, of a captain at Vandenberg Air Force Base in California.

This undated photo released by the U.S. Air Force, shows Lt. Gen. Susan Helms. (Anonymous/AP)

Helms’s 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 called for the firing of Lt. Gen. Craig A. Franklin, 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 publicly revealing why. Neither general was a judge and neither observed the trials, but they intervened to grant clemency before the convictions could be heard by an appeals court.

Helms explained in an internal memo that surfaced only recently that she reversed the jury after reviewing the evidence and finding the captain’s testimony more credible.

Drew Pusateri, a spokesman for McCaskill, said the senator is blocking Helms’s nomination until she receives 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.

A string of abuse scandals

The Air Force has been rattled by a string of sexual-abuse scandals over the past year, including the rape and assault of dozens of recruits by basic-training instructors at Lackland Air Force Base in Texas.

The latest embarrassment struck Sunday, when Arlington County police arrested the chief of the Air Force’s sexual-assault prevention branch and charged him with sexual battery. Police said Lt. Col. Jeffrey Krusinski was drunk when he approached a woman in a Crystal City parking lot and grabbed her breasts and buttocks. Maj. Mary Danner-Jones, an Air Force spokeswoman at the Pentagon, said Krusinski was “removed from his position immediately” when the Air Force learned of his arrest.

Defense Secretary Chuck Hagel called Air Force Secretary Michael Donley to “express outrage and disgust” over Krusinski’s arrest and promise that the matter will be dealt with “swiftly and decisively,” according to a Pentagon statement.

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 say they are reluctant to press charges because they lack faith in the military justice system. Of those cases that are reported, about one in 10 proceeds 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 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.

“When commanders and those in authority set convictions aside, reduce sentences or drop charges, it creates a chilling effect in the system,” said Nancy Parrish, president of Protect Our Defenders, a group that represents victims of sex crimes in the military.

Hagel last month said he would support a legislative proposal to change military law so that commanders could no longer set aside convictions for serious sex crimes. His decision marked a reversal for the Pentagon, which had long resisted the measure. Some lawmakers want more far-reaching legal changes.

A verdict appealed

The case in which Helms overturned the jury finding began in October 2010, when a noncommissioned officer at Vandenberg reported that she had been sexually assaulted by Capt. Matthew S. Herrera in his bedroom after a night of drinking.

Herrera’s housemate told authorities that he had a history of acting aggressively with women, according to the case file obtained by The Washington Post. Investigators found another woman, a second lieutenant, who said Herrera sexually assaulted her in the back seat of a car a year earlier, although she did not report it at the time.

Herrera was charged in both cases. At his court-martial, his attorneys argued that the sexual encounters were consensual. A jury of five Air Force officers found Herrera guilty of sexually assaulting the lieutenant and sentenced him to 60 days behind bars, a loss of pay and dismissal from the Air Force. He was found not guilty of assaulting the noncommissioned officer.

Herrera applied for clemency, arguing that he was innocent and that it would be an injustice to force him to register as a sex offender. Documents show that Helms’s legal adviser urged her to reject Herrera’s request. But in February 2012, the general granted clemency without explanation, erasing Herrera’s conviction.

Soon afterward, the noncommissioned officer who had accused Herrera of sexually assaulting her said that she had crossed paths with him at Vandenberg and, because she was junior in rank, she was required to salute him.

“He had a very smug look on his face,” Tech. Sgt. Jennifer J. Robinson said in an interview. “I was devastated and shocked.”

Herrera did not respond to interview requests placed through his attorney, Richard P. Lasting of Los Angeles.

General’s rationale

Helms declined to comment through an Air Force spokesman. Although the general did not publicly divulge her reasons for overturning the conviction, she wrote a memo for her personal files explaining her decision, said the spokesman, Lt. Col. John Dorrian.

The memo was not made part of the case file or shared with prosecutors, defense lawyers, Herrera or his accusers, Dorrian said. In response to an inquiry, however, the Air Force provided a copy to The Post. It also gave a copy to McCaskill’s office.

In the five-page memo, dated Feb. 24, 2012, Helms wrote that she reviewed the court-martial transcript and trial exhibits. She said she came to the opposite conclusion of the jury and found Herrera to be a more credible witness than the lieutenant. Helms wrote that it was not unreasonable for Herrera to believe that the woman had given implied consent.

“It is undoubtedly true that [the accuser’s] feelings of victimization are real and justifiable,” Helms wrote. “However, Capt. Herrera’s conviction should not rest on [the accuser’s] view of her victimization, but on the law and convincing evidence.”

Instead of sexual assault, Helms found Herrera guilty of committing “an indecent act,” a lesser offense. The Air Force said Herrera was involuntarily discharged in December.