The former chief prosecutor for the Air Force said in a Yahoo News interview that he was “put out to pasture” after he criticized top commanders for interfering with his efforts to convict officers who committed sexual assaults.

Col. Don Christensen served for four years as the Air Force’s top prosecutor, winning a series of major sexual-assault cases, including the high-profile conviction of Lt. Col. James Wilkerson, a decorated F-16 pilot and the inspector general of Aviano Air Force Base in Italy.

But Christensen, 53, said he recently made an agonizing decision to retire — and accept a new job as president of a civilian advocacy group, Protect Our Defenders — after being reassigned to a new position following a series of clashes with Air Force brass.

Those clashes began last year when he started speaking out — and briefing members of Congress — about his objections to the controversial decision of a top Air Force general to overturn Wilkerson’s conviction. The case set off a firestorm on Capitol Hill over rules that, at the time, empowered commanders, who served as the “convening authority” in court-martial cases, to overturn jury verdicts.

“My reaction was that this was the final straw, that we were going to lose military justice, that Congress would be outraged, I was outraged, and that this was the death knell to the justice system as we knew it,” Christensen said in the interview about the decision by Lt. Gen. Craig Franklin, then the commander of the Third Air Force in Europe, to wipe out Wilkerson’s conviction for sexually assaulting a female physician’s assistant in his home.

Air Force Lt. Col. James Wilkerson. (U.S. Air Force)

In the months after criticizing the decision, Christensen — who had been previously evaluated by his supervisors as the “top litigator in the Air Force” — received what he viewed as a downgraded personnel report. Then this summer, he said, he was removed from his position as chief of the Air Force prosecution office and directed instead to take what he considered to be a far less meaningful position as a judge on an Air Force appellate court, a job he had never sought and didn’t want. “I felt like I was going to pay a hell of a price” for speaking out, he said.

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“Absolutely not,” Col. Chuck Killion, the director of the Air Force judiciary, which oversees the service’s prosecution office, said in an interview, when asked whether Christensen was subjected to any retribution because of his outspoken criticism of the role of military commanders in sexual-assault cases.

He said Christensen’s reassignment this year to the Air Force Court of Criminal Appeals was part of a normal rotation, noting that those in the colonel’s position “typically serve two to three years, [and] Christensen had served for four years.”

Christensen’s blunt comments come as the U.S. military faces a one-year deadline from President Barack Obama, which expires this week, to provide the White House with a report detailing how it is making “substantial improvements” in its responses to sexual assault.

They also come amid a series of new cases roiling the military, including allegations of sexual misconduct at the Air Force Academy and reports of retaliation against whistleblowers there, as well as recent convictions of officers at Fort Leonard Wood in Missouri, Ellsworth Air Force Base in South Dakota and Spangdahlem Air Base in Germany.

Partly in response to the uproar over the Wilkerson case, Congress has already stripped commanders of their authority to overturn jury verdicts. But the new cases, and the continued problem of sexual assaults, have led to a new push for legislation sponsored by Sen. Kirsten Gillibrand, D-N.Y. — with support from conservative Republicans like Sens. Rand Paul of Kentucky and Ted Cruz of Texas — that would further overhaul the military-justice system, removing commanders from any role in prosecution decisions and creating instead an independent prosecution office.

Senate Armed Services Committee member Sen. Kirsten Gillibrand, D-N.Y. listens on Capitol Hill in Washington, Tuesday, June 4, 2013, during the committee's hearing on pending legislation regarding sexual assaults in the military . (Susan Walsh/AP Photo)

Christensen, in his new role as an outside advocate, is due to appear at a Capitol Hill press conference on Tuesday with Gillibrand in support of her bill.

Asked if he viewed himself as a whistleblower, Christensen replied: “I hate that term in a lot of ways because you feel like you’re doing something that is disloyal. I don’t feel like I’m being disloyal to the Air Force. I feel like I’m being loyal to the Air Force by helping us solve a huge problem.”

He also said his decision to retire and give up his officer’s commission, after 23 years in the Air Force, was a painful one, especially given a rich family history of service. His father was a navigator who flew more than 100 combat missions during the Vietnam War, and his grandfather was an Army Air Corps intelligence officer during World War II.

“Between myself, my dad and my grandfather, we’ve dedicated 70 years to the Air Force,” he said. “I love the Air Force. But the Air Force is failing, the Department of Defense is failing. And — I knew that I had to step out.”

Christensen, who directed an office with 18 senior trial lawyers and five appellate lawyers, says his run-ins with top Air Force commanders began last year when he was contacted by this reporter (then with NBC News) about the dispute over Franklin’s decision to free Wilkerson despite a court-martial verdict convicting the pilot of sexual assault and sentencing him to a year in confinement.

Wilkerson’s lawyer, who denied the charges on his behalf, said his client’s accuser, Kimberly Hanks, had “lied about multiple aspects of the case.” Franklin, in a letter explaining his decision, had also raised questions about the accuser’s credibility and cited Wilkerson’s background as a “doting father and husband.”

This undated image provided by Protect Our Defenders shows Kimberly Hanks. (Protect Our Defenders/AP Photo)

But Christensen, who personally prosecuted the case, said Hanks (who agreed to be publicly identified last year) was “one of the most credible witnesses I’ve ever dealt with” and that her account of being assaulted by Wilkerson was “100 percent consistent.”

Christensen was then asked by Rep. Jackie Speier, D-Calif., a member of the House Armed Services Committee, to brief her about the case. No sooner did he do so than, Christensen said, he got a phone call from Lt. Gen. Richard C. Harding, then the judge advocate general, telling him that “I was not to do it anymore, that they didn’t want me talking to members of Congress, they didn’t want me talking to the media.”

The Air Force judge advocate general’s office later “did back off” because, said Christensen, “the law is not on their side. But the initial conversation was, ‘Stop. Don’t do it again.’”

Efforts to contact Harding, who retired from the Air Force this year, were unsuccessful. But Killion, whose office oversees the judge advocate general’s office, said Christensen “was never directed not to talk to members of Congress or the news media. He was told not to go in uniform if he was sharing his personal opinion.”

(Speier said in an email statement that she reached out to Christensen on her own initiative and called his resignation “a huge loss to the Air Force and the survivors he served.”)

But Christensen said his problems didn’t end there. He received instructions via email from the judge advocate general’s office recommending that he support what was then the official Air Force position on the authority of commanders to overturn verdicts. Christensen said he couldn’t do so in good conscience, and not just because of Franklin’s action in the Wilkerson case: He had also seen, in vivid terms, how the influence of commanders distorts military justice, especially in sexual-assault cases, he said.

“One of the dirty little secrets of military justice is what happens in that courtroom,” Christensen said, “when you have the prosecution on one side of the courtroom and the defense on the other side, and a victim is sitting on the witness stand telling the jury what happened, and she looks out over that courtroom, she looks behind her rapist and she's going to see her commander sitting behind her rapist. She’s going to see her first sergeant sitting behind her rapist. She's going to see her squadron leader sitting behind her rapist. That's what we have to overcome.”

Lt. Gen. Craig A. Franklin. (af.mil)

That’s what happened in one recent case at Ellsworth Air Force Base, he said, in which a female pilot, a major, accused a captain in her squadron of sexually assaulting her.

At the trial — prosecuted by Christensen’s office — “the commander testified for the accused. Her fellow fliers testified for the accused.” The captain was still convicted, but as he was awaiting sentence in the courtroom, with the major present, Christensen said, the squadron commander “gives the guy who sexually assaulted her a hug.” The clear message to other victims, he said, is “don’t report. Don’t report.”

Killion said the squadron commander at Ellsworth denies hugging the defendant in that case. He also said the case — which led to the conviction and discharge of the offender — shows “the system worked with the involvement of commanders and JAGs [judge advocate generals]."

Maj. Gen. Gina Grosso, director of the Air Force Sexual Assault Prevention and Response Office, said the service has made major improvements in its handling of sexual-assault cases, noting that there has been a 126 percent increase in the past three years in reports of misconduct — a sign that victims feel more comfortable reporting abuse.

“We do believe commanders are at the center of gravity to really take on this problem,” she said.

Christensen said he got his own message earlier this year when he was removed from his job and directed to take a position on the appellate court — a post he viewed as essentially meaningless, since, given his previous role as top prosecutor, he would have to recuse himself from most cases before the panel.

He also said a new personnel report he received earlier this year was less glowing than his previous one ranking him as the Air Force’s best litigator. Although still positive — it called him an “A-plus litigator,” he said — he viewed it as containing pro forma language, with a subtle but unmistakable meaning.

“When I got my performance report, I knew they were sending me a message that — they didn’t want me in the Air Force anymore,” he said.

Killion said he could not discuss Christensen’s personnel evaluation because it would violate the Privacy Act. But asked about the colonel’s performance as the Air Force’s top prosecutor, he said: “He did a good job.”