An Air Force general’s decision to overturn the conviction of a standout fighter pilot on sexual assault charges is stirring anger on Capitol Hill, where some lawmakers say they are losing patience with the military after a string of related scandals.

Several members of Congress have demanded that the Pentagon intervene after Lt. Gen. Craig A. Franklin, commander of the Third Air Force in Europe, ordered the release of the fighter pilot from prison on Feb. 26 and tossed out his conviction without explanation.

The pilot, Lt. Col. James Wilkerson, had been found guilty in November by an all-male jury at Aviano Air Base in Italy in what was seen as a test case of the Air Force’s willingness to tackle such crimes. But the decision to grant him clemency has infuriated many female lawmakers and advocacy groups, who said the outcome will discourage victims from reporting abuse.

“The appearances of this are devastating to victims of sexual assault throughout the military,” said Sen. Claire McCaskill (D-Mo.), a member of the Armed Services Committee and a former prosecutor. “It looks like somebody taking care of one of their guys.”

The Air Force has been grappling for the past year with an even bigger scandal in which basic-training instructors were charged with raping and assaulting dozens of female recruits at Lackland Air Base in Texas. Air Force leaders have bluntly described sexual misconduct as a “cancer” in the ranks that the service is struggling to combat.

Other branches of the armed services are experiencing similar problems. The Senate Armed Services Committee is scheduled to hold a hearing Wednesday on sexual assault problems in the military, the first time it has devoted a session to the subject in a decade.

The number of reported rapes, sexual assaults and cases of harassment has soared in recent years even as the Defense Department has adopted new programs to aid victims and crack down on perpetrators. Although military leaders say they have improved their handling of such cases, a Pentagon report last year estimated that only about one-sixth of victims report the crimes.

Advocacy groups said that the decision last month to overturn the jury’s verdict will only deepen concerns about the system.

Franklin, a three-star commander based in Germany, is not a judge and did not observe the trial. But as the senior officer in Wilkerson’s chain of command, he had final authority in the court-martial process. Air Force officials said he reviewed the entire trial record as well as a clemency appeal from the defendant and a personal letter from the accuser. He concluded that there was “insufficient evidence to prove guilt beyond a reasonable doubt” and decided he “could not, in good conscience, sustain the conviction,” according to Lt. Col. Paul D. Baldwin, an Air Force spokesman.

Franklin did not elaborate, and he declined a request for an interview. Under military law, a commander in his position has the authority to reduce a sentence or dismiss a conviction and is under no obligation to give a reason.

Baldwin said that the general, who is also a pilot, “does not personally know” Wilkerson and does not recall interacting with him socially or professionally.

It is very rare for a commander to grant clemency and dismiss a case entirely. Over the past five years, Air Force prosecutors have recorded 327 convictions for rape, sexual assault and similar crimes. Of those, five verdicts were overturned by commanders based on clemency, the Air Force said.

In a letter, McCaskill asked Air Force Secretary Michael B. Donley and Gen. Mark A. Welsh III, the Air Force chief of staff, to consider firing Franklin. “I just think the system is messed up if a general can overturn a case like this with a stroke of a pen,” she said. “That’s just offensive to anyone’s sense of justice.”

Two other senators, Barbara Boxer (D-Calif.) and Jeanne Shaheen (D-N.H.), sent a letter to new Defense Secretary Chuck Hagel last week asking him to review the case as well.

In an interview, Shaheen said she was still “waiting for all the facts” but was disturbed by appearances.

“This is a case that sends absolutely the wrong message,” she said.“If we’re going to continue to attract women into the military, which we need to do to have the best and brightest, then we need to address this.”

George Little, a Pentagon spokesman, said Hagel would deliver a response to the senators soon, adding: “The secretary has made it clear that sexual assault has absolutely no place in our armed forces and must be addressed decisively.”

Under military law, no one in Air Force or the Defense Department has the authority to overrule Franklin’s decision. Nor can prosecutors appeal.

Lt. Gen. Richard C. Harding, the Air Force’s judge advocate general, said the legal authority for a commander to grant clemency dates to the birth of the American armed forces in 1775.

Harding said the military has always given commanders the power and discretion to do what is necessary to uphold “good order and discipline,” the foundational traits for the armed forces. “Those aren’t empty words.”

He said it was common for commanders, who are accustomed to giving orders without being questioned, not to divulge their reasoning in a clemency case.

The Wilkerson case attracted intense interest inside the Air Force when it went to trial in November, largely because the defendant was an officer whose personnel evaluations had branded him a “superstar.”

Wilkerson, 44, was an F-16 fighter pilot who had flown missions in Afghanistan and Iraq, and was serving as the acting inspector general at Aviano Air Base. He was charged with assaulting a 49-year-old woman, an independent civilian contractor at the base, who had met him at a party.

According to testimony reported by Stars and Stripes, a newspaper that covers military affairs, the woman said she had gone to sleep alone in Wilkerson’s guest bedroom but awoke at 3 a.m. to find him groping her breasts and vagina.

Wilkerson denied the allegations and said he was asleep in his own bed the entire night. The case rested largely on circumstantial evidence and pitted the word of the accuser against testimony from Wilkerson’s wife, who said she kicked the woman out of the house without her shoes in the middle of the night because she was too noisy.

The military jury convicted Wilkerson of aggravated sexual assault and sentenced him to a year in prison.

In an interview, the accuser said the trial was emotionally wrenching but that the Air Force treated her fairly and with respect. “The prosecution was behind me 1,000 percent,” she said.

But she said she was stunned when prosecutors informed her that Franklin had thrown out the conviction without giving a reason. “I found that absolutely shocking,” she said, calling it “a prime example of the old boys’ network. It’s cronyism through and through.”

The Washington Post generally does not identify victims of sexual assault and the woman asked that her name be withheld. She contacted The Post through an advocacy group, Protect Our Defenders, that represents sex-crime victims in the military.

Wilkerson was freed from the military brig in Charleston, S.C., and is now on leave as he prepares to return to active duty.

The general’s decision to grant clemency came as a “surprise” to Wilkerson given the military’s recent crackdown on sex crimes, said his attorney, Frank J. Spinner.

“It is exceedingly difficult in this environment involving sexual assault cases,” Spinner said. “We see this decision as restoring some integrity to the process.”

Some lawmakers and victim advocacy groups, however, argued the opposite.

Rep. Jackie Speier (D-Calif.), a member of the House Armed Services Committee, said she would introduce a bill next week to strip commanders of their power to overturn legal decisions or reduce sentences imposed by military judges and juries. Such actions, she said, “make a mockery of the entire legal system.”

“The laws that are on the books . . . are so antiquated and so rigged in favor of the assailant that frankly it’s no wonder someone won’t report” a sex crime, Speier said in an interview.