U.S. soldiers on patrol in Afghanistan in 2012. (1st Lt. Jason Uhlig/ U.S. Army)

Nearly two-thirds of the 91,764 U.S. troops who were separated from the military for misconduct in a recent four-year period had been diagnosed with post-traumatic stress, a traumatic brain injury or another condition that can lead to misconduct, according to a report released Tuesday, raising questions about the Pentagon’s treatment of combat veterans.

The Government Accountability Office found that the Defense Department needs to take action to make sure that commanders appropriately consider medical conditions when weighing what to do with service members facing misconduct allegations. Some 57,141 troops were separated from the service despite a potentially relevant diagnosis between 2011 and 2015, and 13,283 of them received other-than-honorable discharges that could prevent them from receiving care from the Department of Veterans Affairs, the report said.

The report was required by Congress in a 2015 provision in the National Defense Authorization Act. Unless policy inconsistencies are resolved, the GAO said, “the risk increases that service members may be inappropriately separated for misconduct without adequate consideration of these conditions’ effects on behavior, separation characterization, or eligibility for VA benefits and services.”

The Pentagon also “has little assurance” that service members who have been diagnosed with post-traumatic stress or traumatic brain injury will receive required screening and counseling before they are separated, the report said.

David Smith, the acting assistant secretary of defense for health affairs, expressed “serious concerns with the accuracy and clarity of the data” that the GAO analyzed in a March 24 letter submitted to investigators and included in the report.

The numbers of total separations and service members diagnosed with post-traumatic stress or traumatic brain injury and the kinds of conditions included in the report combined to “greatly exaggerate” the number of service members separated for misconduct, Smith wrote. The GAO also counted each individual who had both post-traumatic stress and a traumatic brain injury as two people, he said.

“As such, the inflated figures create the false impression that the majority of service members administratively separated for misconduct had psychological health conditions that would explain their misconduct,” Smith wrote.

The GAO stood by the data. The agency said that a discrepancy in separations that Smith noted stemmed largely from the Army and Marine Corps providing numbers that included service members who left active duty to join the National Guard or reserve duty, while information provided by the Defense Manpower Data Center — which oversees personnel statistics for the Pentagon — did not. The individual armed services confirmed that the data center’s numbers are accurate, the GAO said.

The GAO also denied that there was any double-counting of affected troops involved and noted that it had clarified the point in the final draft of the report.

Of all troops discharged after misconduct between 2011 and 2015, 35 percent had some form of adjustment disorder, 29 percent had an alcohol-related disorder, 22 percent had a depressive disorder, 20 percent had a substance-abuse disorder, 17 percent had an anxiety disorder, 11 percent had a traumatic brain injury and 8 percent had post-traumatic stress. The last 6 percent included personality disorders (4 percent) and bipolar disorders, the report said.

The GAO recommended several changes that the Pentagon supported, including that the Air Force and Navy change their screening policies for post-traumatic stress and traumatic brain injury to bring them in line with the rest of the Defense Department.

The Pentagon also agreed that the services should routinely monitor the screening of troops who face potential discharge for misconduct, counsel troops about VA benefits and train service members how to identify signs of mild brain injuries, the report said.