An Air Force general at the center of criticism of the military’s sexual assault policies is stepping down as the Pentagon works to clean up its ranks under the close watch of President Barack Obama and Congress.

Lt. Gen. Craig Franklin will step down at the end of the month from his post as the commander of the Third Air Force amid questions that he’s mishandled prosecutions in two sexual assault cases.

In the most high-profile case, Franklin last spring overturned the jury conviction and sentence of a fighter pilot. His decision prompted an outcry from lawmakers who said he was protecting one of his men and led to major legislative changes to the military’s World War II-era justice system.

The annual defense authorization bill just signed by the president orders up more than two dozen changes to Pentagon sexual assault policy, including removing a commander’s authority to change the outcome of legal verdicts and reducing sentences. Obama has given the Pentagon until December to make “substantial improvements” in its handling of sexual assault cases. Otherwise, he may force major changes, including removing commanders from prosecution decisions entirely.

In a prepared statement, Franklin said he was ending his nearly 37-year military career because his judgment had been “questioned publicly regarding my decisions as a general court martial convening authority.”

( PHOTOS: Scandal pols: Where are they now?)

“This is a distraction for the Air Force and for my role as a general court martial convening authority,” he said. “The last thing I want in this command is for people to feel they cannot bring a sexual assault case forward, or feel it won’t be dealt with fairly. In addition, public scrutiny will likely occur on every subsequent case I deal with.

“I am concerned this could jeopardize the privacy of both the victim and the accused,” Franklin added.

Democratic Sens. Claire McCaskill of Missouri and Kirsten Gillibrand of New York, two prominent Armed Services Committee members pushing the sexual assault debate, had called for Franklin’s firing over his decisions, including a second case last summer in which he declined to prosecute a rape allegation.

“Lt. Gen. Franklin’s decision to resign is the right one,” McCaskill said. “His handling of sexual assault cases is the best possible illustration of why civilian review, elimination of commanders’ ability to overturn convictions and so many other protections are included in our recent defense bill.”

( PHOTOS: Top congressional scandals)

Gillibrand, who is still pushing more sweeping changes to Pentagon policy that would entirely remove commanders from the prosecution system, said Franklin’s retirement “is a glaring admission that untrained, biased commanders should not have this authority.”

“I am pleased that Lt. Gen. Franklin will no longer serve in his post — but take no joy in this outcome, as it’s a painful reminder for the victims of military sexual assault that the deck is stacked against justice when commanders hold all the cards,” she added.

Gillibrand may get a Senate floor vote on her legislation as early as next month, according to a Senate Democratic leadership aide.

Franklin is the second recent high-profile Pentagon official tied to sexual assault issues to leave their job. Maj. Gen. Gary Patton, a 35-year Army veteran, is retiring this spring amid an internal investigation that he intimidated whistle-blowers during a previous stint in Afghanistan. Most recently, he was director of the Sexual Assault Prevention and Response Office.