An Afghan warlord backed by US special forces faces persistent allegations that he launched a two-year spate of violence involving burglary, rape and murder of civilians, desecration of mosques and mutilation of corpses. Yet, despite repeated warnings about the atrocities Commander Azizullah is alleged to have committed, he has remained on the payroll of the US military as an "Afghan security guard", a select band of mercenaries described by some as "the most effective fighting formation in Afghanistan".

Interviews with religious leaders, tribal elders, villagers, contractors and Western and Afghan officials all pointed to a reign of terror in which they believe 31-year-old Azizullah, a ethnic Tajik, targeted Pashtun civilians while fighting the Taliban. Although individual allegations, all from ethnic Pashtuns, might be inaccurate, malicious or motivated by envy of Azizullah's close and lucrative links to US special forces, taken together they come from sources belonging to a range of tribes and from several areas. The testimony also tallied with several independent reports documenting the allegations against Azizullah and seen by The Independent, including two confidential reports compiled by UN officials and circulated to Nato personnel last year.

A Nato spokesman said that its own investigation of Azizullah turned up nothing. "There was a derogatory report via UN channels last summer, but when we tried to research it, there was really little information to substantiate what were essentially claims," said Lieutenant-Colonel John Dorrian, chief of operations at Nato's public affairs unit in Kabul. "As a matter of due diligence, we subsequently tried to backtrack to the origin of the claim, but nothing credible could be found."

Human rights experts say that is not necessarily surprising. The coalition "in general has been slow to the mark in developing transparent, public, and thorough accountability structures", said Erica Gaston, a human rights lawyer for the Open Society Foundations. "It's getting better, but there's still a lot of foot-dragging.

"And when it does investigate, it doesn't bring a great deal of healthy scepticism to examining the first version of events given. Often an investigation will comprise statements by the commanders or troops on the ground, perhaps a review of video or other signal intelligence, and that's it. That's not a bad methodology to start out with, but if you really want to get the whole story on accusations of misconduct, particularly when they involve local warlords, you need to get out and talk to the community. That just isn't how Isaf investigations work generally."

The allegations of persistent abuses are embarrassing for Nato, and not just because of the closeness with an alleged war criminal. They also showcase the big-gest drawbacks of militias, which US commander General David Petraeus wants to expand aggressively across Afghanistan. He wants to triple the size of "local defence initiatives" [militias] to 30,000 members nationwide. Local community representatives have described the plan as "sending villagers to the front line".

Analysts in Kabul also say that although the plan may temporarily help dent the Taliban, the consequences are too awful to contemplate: resurgent warlords, deepening ethnic tensions, widespread bloodletting and the erosion of what little authority the government in Kabul has left. The cost of some short-term success in the military fight against the Taliban could, over time, see a return to Afghan-istan's darkest days.

UN officials first raised the subject of Azizullah with Nato in February 2010, when a report landed on the desk of US Lieutenant-General David Rodriguez, Nato's deputy commander in Afghanistan. It warned of "grave dissatisfaction with the way in which SOF [Special Operations Forces] operations are conducted and... doubts about the positive impact of SOF 'local defence initiatives'."

The report cited a complaint by Afghan villagers that during a special forces night raid on 7 January 2010, in which six civilians were killed, "an Afghan security commander, by the name of Azizullah, and the men under his command [stole] about $9,600 belonging to three of the killed civilians".

By the summer, the US military had received a more comprehensive list of the atrocities Azizullah was accused of, compiled by Western and Afghan officials lobbying for his removal, and begun looking into the complaints.

A report entitled Evidence against Azizullah stated: "We strongly recommend that this man be removed from his position working in the services of the US military. Numerous complaints have been made to us in recent weeks regarding the behaviour and activities of Commander Azizullah. Elders from a number of districts... have provided independent accounts of Azizullah's involvement in criminal activities (theft), indiscriminate killings and more sordid activities such as detaining young boys... holding them for several weeks [and] sexually abus[ing] them.

"Clearly, it is difficult to confirm the veracity of information provided to us by local community representatives, and there may even be cases where it is inspired by malice towards the government or security forces, but there is an undeniable pattern regarding this individual that cannot be disregarded. We see significant indications that the unintended consequences of employing someone like Commander Azizullah may be the growing hostility of large parts of the population."

The report also warned that as long as special forces continued to act on tip-offs from Afghan sources, some of those sources would feed them false information "to frighten local people into keeping quiet about blatant instances of corruption [and] immoral behaviour, as well as for settling scores. We believe, in the light of so many independent reports, this to be the case with Commander Azizullah".

But by October, and unable to substantiate any of the allegations against Azizullah, his benefactors dropped the issue. Colonel Dorian added: "As always, if there is credible information of wrongdoing, we encourage anyone with such information to take it to the cognisant authorities so it can be fully and properly adjudicated."

Commander Azizullah rubbishes the claims. "Since the Taliban and al-Qa'ida couldn't kill me with their suicide attacks or landmines, they're now using propaganda against me. I have never killed anyone innocent. I'm a very religious person; I respect my religion, so how could I desecrate a mosque or kill a civilian? [...] You won't find a single person who can prove that I've done anything you mention, like raping boys, desecrating mosques or killing innocent people."

During the interview, the leader of the US special forces detachment supporting Azizullah, who called himself Dan, came on the phone. "We've gone a huge way as far as collateral damage and civilian casualties [go]," he said. "That's gone down quite a bit. We have quite a bit of control over our partner's force and... we do everything we can to [avoid civilian casualties]. There's been really no civilian casualties, at least since I've been here."

Azizullah comes from a generation of Afghans growing up knowing nothing but fighting. Life as an ethnic Tajik was hard under the predominantly Pashtun Taliban regime. "The Taliban were disturbing me a lot, they weren't letting me live a normal life," he said. "And after the collapse of the Taliban I became a soldier here in Urgun [district]."

Azizullah claims to have survived between 10 and 20 attempts on his life, and was wounded in recent fighting. He said he has "conducted lots of operations, seen lots of stuff, been blown up by a suicide bomber in 2006".

That blast, which killed his cousin Sardar and several comrades, was a difficult blow. "I wasn't only upset about my cousin," he said. "There were 18 people killed in that incident. Every individual that was killed was [like] Sardar to me."

The Tajiks and Afghanistan's ethnic faultlines

The widespread stories of Azizullah's activities also seem to have stoked ethnic tensions between the small Tajik minority he comes from and the Pashtun majority in the area.

Such tensions have created one of the biggest fault lines dividing Afghanistan, and some argue that much of the violence of the past 30 years has been carried out as part of a war between the country's large Pashtun minority, on one side, and the country's ethnic Uzbeks, Hazaras and Tajiks on the other.

A Pashtun cleric said that friction between the Tajik and Pashtun communities in eastern Paktika province, where Azizullah operates, had never been so high.

A Western contractor with first-hand knowledge of the area said: "Tajiks... say the guy is a national hero. [However] they also say, 'We'll pay for that'. If the coalition leaves they'll have to leave too. They disapprove of his actions. If you send a Tajik as sheriff to a Pashtun area you're bound to fail. It's a very ethnically polarised area."

There are certainly reasons for some Afghans to want to slander Azizullah, who is reputed to use his links with Nato to broker contracts and take a cut of the spoils.