The backdrop for the downsizing is a fiscal crisis. Four years ago, Defense Secretary Robert M. Gates said health care costs were “eating the Defense Department alive”; last year, they represented almost 10 percent of the defense budget. Close to half of the beds in military hospitals appear to sit vacant, significantly more than the civilian hospital average.

Behind those fiscal woes, though, is a hospital system at odds with itself, struggling with conflicting missions that, according to many people interviewed, put not just the Pentagon’s coffers but the quality of care and patient safety at risk.

Pentagon health leaders say their hospitals’ paramount mission is military: to hone the skills that doctors and nurses will need in the carnage of combat. But their principal business is both broader and more mundane: They are essentially community hospitals, providing a smorgasbord of low-cost primary and specialty care, from births to breast implants to appendectomies.

Especially, but not only, at smaller hospitals, the military priorities undercut the day-to-day delivery of health care, doctors and nurses say.

Inexperienced doctors often assume outsize responsibilities because military policies encourage more experienced and ambitious clinicians to become administrators. Continuity, so crucial to medical care, is lost as hospital commanders and doctors, as well as patients, constantly rotate from post to post. The wars in Iraq and Afghanistan have taken an especially heavy toll: With many military doctors and nurses overseas, hospitals have been forced to shunt patients to civilian care, leaving empty beds and out-of-practice medical staffs.

Resistance to Proposed Cuts

To some veterans of the system, the inherent incongruities raise the question of whether, with limited exceptions, the military should even be in the hospital business.

“It’s a dangerous game,” said John Schafer, who served for eight years as deputy commander for clinical operations at Reynolds Army Community Hospital at Fort Sill in Oklahoma. “It is crazy that the military doesn’t say, hey, we are really good at outpatient medicine and this inpatient thing is out of our league.”