Ms. Gilbert’s experience was described in an article in The New York Times in December that detailed numerous cases of military physicians, nurses and other health care workers whose careers were damaged after they complained about lapses in safety or quality of treatment. The hospital workers contended that they had been pushed out of their jobs, transferred, given pay cuts and punished with negative evaluations after reporting weaknesses in care to their superiors.

The inquiry found that after Ms. Gilbert contacted the Joint Commission, her supervisors barred her from meeting with the hospital inspectors, kept her in the dark about the lapses that were identified and prevented her from helping to correct them.

At the time, “she was the only person in the infection control section who was qualified to work on infection control,” said Nick Schwellenbach, the special counsel’s spokesman. “If she was not sidelined, she could have helped the hospital fix the problems more quickly.”

Instead, her immediate supervisor cut her hours in half. Then the Army charged her with being absent without leave because she had not requested leave for the hours that were cut from her schedule, the inquiry found.

Later, Brig. Gen. Robert D. Tenhet, the medical commander for the region encompassing Womack, wrote her a letter saying co-workers had characterized her as an obstructionist who was “very difficult to work with” and who had withheld information. She was transferred to a clerk’s job, with no duties. Eventually, she was told that she would be fired for improperly accessing a patient’s information.