Center for Strategic Communication

.S. Marine Corps Lance Cpl. Lance Souders with 1st Battalion, 9th Marines shows an Afghan police officer how to use a metal detector, Helmand Province, Nov. 18, 2011. Photo: U.S. Marine Corps

The U.S. defense chief announced on Thursday that the U.S. troops have returned to their “normal partnered operations” with their Afghan counterparts, after a recent policy shift put a big layer of bureaucracy in between Americans and Afghans. Only that policy remains in place, the Pentagon confirms.

Defense Secretary Leon Panetta told reporters on Thursday that “temporary adjustments” to low-level joint U.S.-Afghan patrols, enacted in the wake of widespread protests over an anti-Islam video, had mostly come to an end. “I can now report to you that most [U.S. and allied] units have now returned to their normal partnered operations at all level,” Panetta said.

The shift was intended, as Panetta said, to “protect our forces” — not just from anger at the video, but from a broader problem. Afghan forces have killed at least 52 of their American mentors this year. The NATO military command in Afghanistan isn’t totally sure why, and blames a mix of specific Afghan grievances and Taliban infiltration. So last week, the command decreed that the two-star generals at regional headquarters have to approve all joint U.S.-Afghan operations below the battalion level — which accounts for most of them.

Yet although Panetta said the tempo of operations has mostly returned to normal, the two-stars still have to approve the operations themselves. “The FRAGO [fragmentary order] that directed approval for partnered operations below the battalion level be maintained at the R.C. [Regional] Commander-level remains in effect,” says Air Force Lt. Col. Jack Miller, a Pentagon spokesman. Marine Col. David Lapan, the spokesman for the chairman of the Joint Chiefs of Staff, confirmed that the directive is still on the books.

If that sounds bureaucratic, it should. The reason for the shift is to create a layer of protection for U.S. troops against the newly urgent “insider” threat from the Afghan troops they mentor. If the threat is so great that a general in charge of securing vast swaths of Afghanistan thinks an operation at the company, platoon or squad level needs to be shut down, the theory goes, that ought to save American lives.

And it might. But it also creates a complication for the U.S. ticket out of Afghanistan. An unknown but large number of those operations occur below the battalion level, and they occur precisely so that the Afghans will be proficient enough soldiers by 2014 as to take over the war from the Americans. Placing a thick layer of bureaucracy between Afghans and Americans — it’s a big jump between battalion-level command and regional command — “makes no sense if you’re on the ground,” a former U.S. Army mentor to the Afghans told Danger Room last week.

The Pentagon and the NATO military command in Afghanistan have portrayed the edict as a temporary measure in response to the video riots. But they’ve also conceded it’s about the deeper problem of Afghan troops attacking their American mentors. The former is a limited problem that will fade over time. The latter shows no sign of going away. And the persistence of the insider threat goes a long way toward explaining why the NATO military command will still require two-stars to approve joint operations for captains and lieutenants.

It’s possible that the problem remains hypothetical. Maybe the generals can move swiftly enough not to impede the Afghans’ hands-on training. Army Gen. Martin Dempsey, the chairman of the Joint Chiefs of Staff, who returned from a trip to Afghanistan on Wednesday, said there’s no daylight between Afghans and Americans on ending the insider threat. “As one Afghan army commander told me, insider attacks are an affront to their honor, at odds with their culture and their faith,” Dempsey told reporters.

Not every Afghan agrees. A 20-year old Afghan soldier told The New York Times on Wednesday, “We would have killed many of [the U.S. troops] already, but our commanders are cowards and don’t let us.” That’s the kind of quote that gets a two-star general racing to review his low-level commanders’ schedule for patrolling, eating, and sleeping alongside the Afghans.