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The young man seemed to be the perfect recruit for the Afghan National Army. He was smart and motivated and, more important, from a part of the country that had felt alienated from the U.S.-backed regime in Kabul for way too long. So Nangyalai Talash, born and raised in the restive province of Maidan Wardak, was quickly signed up by NATO and the Afghan government in their drive to create a bigger, more self-sustaining and integrated military.

For three years, he proved a good soldier. Talash earned enough trust to be enrolled in a three-month course offered by American trainers who taught him to analyze intelligence and conduct the night raids that had been having a devastating effect on the Taliban. After his graduation, he worked at the headquarters of the Afghan Ministry of Defense in Kabul. Then, suddenly, a few months ago, Second Lieutenant Talash defected to the Taliban.

Or rather, he returned to the Taliban. Before he enlisted, Talash was an insurgent in Maidan Wardak. It turns out that he is a cousin of Mullah Farid Qiam, a prominent Taliban commander in their home district of Sayed Abad, about 75 km outside Kabul, and the leader of many attacks on the strategic Kabul-Kandahar highway, which cuts through Wardak. Perhaps the officials in charge of vetting recruits had been comforted by the fact that Talash's uncle ran oil tankers as a contractor for coalition forces. In any case, that blood tie proved weaker than the other. A few weeks ago Talash, an accomplished gunner trained by the U.S., was heard on a radio ordering his men to target the third black tanker stuck in traffic in Sayed Abad — a vehicle his uncle owned. It went up in flames.

The tale of Talash has been confirmed by several intelligence sources. But allegations of Taliban infiltration of the Afghan army, police and government abound. Even as the so-called green-on-blue incidents grab headlines with details of Afghan soldiers turning on their erstwhile comrades in arms, the Taliban has found ingenious ways to insinuate itself into Afghanistan's bureaucratic dysfunction. "The Taliban know well the weak points of the [Afghan] government, and they know how to exploit those," a senior police official says. The infiltration, he adds, "is very systematic." The green-on-blue killings are alarming the U.S. military, which is already watching its back as it prepares for the 2014 withdrawal. The resulting lack of trust has gotten in the way of the creation of a self-sustaining Afghan security force via joint operations and U.S. trainers. But the broader Taliban infiltration of the government of President Hamid Karzai may prove to be more devastating for the regime's security.

The beefing up of the Afghan National Army's numbers has much to do with the infiltration crisis. In 2007, Afghanistan had roughly 45,000 soldiers and 60,000 police. By October 2011, those numbers had swollen to 170,000 and 134,000, respectively. There has also been a move to increase the presence of Pashtun like Talash in the army. That group forms a majority in the lands in which the war against the Taliban was being waged. "The way they went about it — the pace they did it — was problematic," says Amrullah Saleh, Karzai's intelligence chief from 2004 to '10. For example, as part of a mission to create the force structure of a police district, the militias of two local strongmen were simply called in and added to the payroll of the Ministry of the Interior. Meanwhile, new police recruits were required to provide letters of recommendation from two people — but many came back empty-handed. So, says one recruiting official, "I had some of the soldiers sign recommendation letters for other soldiers. I couldn't come back to Kabul and say I had failed my mission."

It would not have been difficult for the Taliban — perhaps backed by the resources of Pakistan's military intelligence — to take advantage of the flaws in the process. "What easier way to undermine [the armed forces] than to plant a couple hundred [agents] during lax recruitment and have them sit and wait for the appropriate time to strike?" says Abdul Waheed Wafa, the director of the Afghanistan Centre at Kabul University.

Still, Wafa believes that a majority of the infiltrators were assigned not to kill Americans but to preach to fellow Afghans. The behavior of young Western soldiers provided these unofficial chaplains with much fuel to inflame the beliefs of recruits raised as conservative Muslims. "There is no better place to create doubt, question mission and provoke than in the barracks," says Wafa. "We now have soldiers who believe that they will go to hell if they die next to a nonbeliever."

The Taliban has also learned to manipulate the judicial and prison systems. "As soon as police arrest one of them, the Taliban get to work on how to release him," insists a senior police official, who adds, "They have spent a lot of money on this." While there have been allegations that prosecutors have buckled to Taliban pressure and chosen not to charge suspected insurgents, a more potent strategy has been to have sympathizers — among them prominent officials in the Karzai government — petition to transfer Taliban prisoners from jails in the capital to less secure provincial jails. Several high-profile prison breaks from such institutions have taken place recently. Organizing such escapes is not difficult; cell phones are easily smuggled into prisons.

And then there is the role of the tribal elders and their influence on the highest offices in Afghanistan. It was the elders' lobbying that helped cut down the night raids that had set the Taliban back. The U.S.-led raids had resulted in a large number of civilian casualties, and Karzai himself was taken aback by the bloodshed. But some present and former members of his government believe that "stories were exaggerated and dramatized." Says a former senior adviser to the President: "There was a debate ... that there is possibly an element of 'emotional blackmailing' and that some of these elders are influenced or infiltrated by the Taliban."

One governor of a frontline province says he was never consulted by Karzai's office about the identity of the elders who claimed to be from his area of control: "80% to 85% of these elders who come to the President complaining are Taliban sympathizers," he claims. The governor, who asked not to be named because of the sensitivity of his relationship with the central government, continues, "They have created a dangerous parallel system that has the power of getting the President to do anything — to cut back night raids, to release prisoners, to replace commanders." He believes they are taking advantage of Karzai's well-known ambivalence about the war, the President apparently having lost faith in the conflict's purpose and being incensed by what he considers a deliberate U.S. effort to undermine him in recent years. Says one former senior aide to Karzai: "The President has said on many occasions that he no longer believes in America's war against the Taliban."

That kind of talk infuriates the governor, who says the regime is "without a clear vision, without a clear definition of the enemy." He says angrily, "If a soldier opens fire on the Taliban, the elders will tell the President the victim was innocent, and the soldier will go to jail. If he doesn't open fire, the Taliban will."

• Mujib Mashal / Kabul
• The U.S. military may fear turncoat Afghans, but a more systematic subversion is at work