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As the anger over the Koran-burning controversy continued to convulse Afghanistan, another violent incident disrupted how the Kabul government interacts with its Western allies. On Saturday afternoon, a member of the Afghan Interior Ministry opened fire on two U.S. advisers — a lieut. colonel and a major — at the ministry's command-and-control center in the capital. The Americans were shot in the back of their heads as they sat at their desks, news reports said. "A countrywide manhunt is under way for the fugitive," Interior Ministry spokesman Sediq Sediqi told TIME. Since the news broke, speculation has raged over whether the killer was an insurgent infiltrator or simply motivated by the Koran burnings at the Bagram airfield earlier this week. Sediqi denied the idea of infiltration, saying it is "clear that insurgent groups are not able to have such connections as this. The ministry is very secure, and we have not had any such incidents in the past. It cannot be suggested that he has links with some groups. But we will have to investigate."

After reading the initial reports, one Afghanistan-based security expert does not believe the killer was a Taliban plant — as the militant group has claimed. However, Paddy Smith, a security analyst and former British soldier, says, "Given the nature of where the killer was, it is definitely interesting that he was able to holster his weapon and walk away. It is an indication of either confusion or collusion. That's some feat — unless some other people knew about it — to just walk into the control center and head-chop them." But Smith also says the attack underlines huge structural problems facing foreign forces in training a viable Afghan army and security force large enough and strong enough to defend the country from internal and external enemies — one of the requirements the U.S. and NATO have set in order to withdraw by 2014 and still be able to declare a kind of victory.

The growing divide between Afghan soldiers and their mentors has already been stretched to the breaking point after six days of violent and deadly protests over the Koran burning that have left around 30 dead, including four U.S. troops previously killed by Afghan soldiers or men in Afghan-security-force uniforms. The burning of Korans by foreign troops on one side and the killing of foreign troops by Afghan soldiers on the other have pushed the level of alienation between the two sides to what could be an all-time high.

The Saturday murders were only the latest of at least 22 similar killings that have occurred since last April. Smith says there have been at least 35 in the past 12 months, though NATO spokesman Brigadier General Carsten Jacobson refused to confirm that number. The Wall Street Journal reports that at least 77 coalition troops have been killed in the past five years in "green on blue" incidents, with around 57 of those having taken place since early 2010. Smith is not sanguine about improving the situation, even as the allies pour more money and effort into training ever more locals. Says he: "You only ever rent an Afghan, you can't buy one."

"Language and culture barriers always remain," says Smith. "These Americans [killed on Saturday] probably didn't have the first clue of what was about to hit them. Even if the Afghans had been sitting around talking about the murder in Dari [a local language], these guys wouldn't have known about it. Very seldom do we actually connect with each other," Smith says. "These guys are loyal because we pay them. You only start to develop a bond over months and years, and British soldiers only have six months before they go home."

Smith says that NATO troops "get on a plane at a NATO base in the U.S. or Europe and fly to a NATO base in Afghanistan, and they never really engage with the Afghan population. Also — and this is the chicken-and-the-egg question — because of force-protection measures, soldiers can't get out there and win hearts and minds, and because of this, more soldiers die. And the more that soldiers die, the more force-protection measures there are — and they interact even less. We've just driven a wedge between ourselves," Smith says, echoing feelings and observations expressed in numerous conversations TIME has had with analysts, observers, service members, officers and security contractors over more than two years in Afghanistan.

The Saturday attacks seem to verify the findings of a declassified — then reclassified — U.S. Army study titled A Crisis of Trust and Cultural Incompatibility, which was released in May 2011. Through hundreds of interviews with both Afghan and American service members, it found that the murders of NATO troops by Afghan troops "do not represent 'rare and isolated events' as [is] currently being proclaimed." Afghan soldiers cited night raids and home searches by foreign troops, the lack of respect for women, indiscriminate shooting, constant cursing and arrogance as top complaints against their foreign "partners." They also said failure to prosecute foreign troops for war crimes, disrespect for Afghan soldiers, poor logistical support and a failure to share information led to divisions between the two forces — among numerous other complaints that included entering mosques, eating in front of fasting Afghan soldiers during Ramadan and other episodes of the desecration of the Koran.

At the same time, the report noted that U.S. troops have an extremely low regard for their Afghan counterparts. The service members' top complaints were that the Afghans were drug abusers, thieves, traitorous, unstable, incompetent and had poor officers and noncommissioned officers. The troops also said Afghan recruits lacked discipline, were dangerous in firefights, were cowardly, lazy and had poor hygiene.

The report concludes that "the rapidly growing fratricide-murder trend committed by Afghan national security force [ANSF] personnel against NATO members" confirms the "ineffectiveness [of] our efforts in stabilizing Afghanistan, developing a legitimate and effective government, battling the insurgency, gaining the loyalty, respect and friendship of the Afghans [and] building the ANSFs into legitimate and functional organizations." The report says that these complaints and murders challenge the usefulness of the "partnering" concept. "This is all the more a paradox given [NATO's] assumption of and planned reliance [on] the [ANSF] to be able to take over the security burden before it can disengage from this grossly prolonged conflict."

Despite that, the U.S. and NATO have always painted the partnership in positive terms. In a message issued on Saturday, the NATO commander in Afghanistan, General John Allen, thanked the Afghan military "for the sacrifices they have made this week to minimize violence throughout the country," and added that "for many years, these brave ANSF soldiers and policemen have stood together alongside us, shoulder to shoulder, shohna ba shohna, in dutifully seeking to protect the Afghan population from a merciless insurgency." That message was released before the two U.S. troops were killed. On Saturday, NATO pulled back all of its troops from their mentoring roles in Afghan government ministries, a significant move that NATO spokesman Jacobson described to TIME as "temporary" — but one that is bound to have far-reaching ramifications over the coming year.

• John Wendle / Kabul
• The death of two American military officers allegedly at the hand of an Afghan colleague deepens a crisis that continues to weigh on the country