In nearly nine years of warfare in Afghanistan, U.S. Special Forces have done their fighting in the shadows, governed by rules largely of their own making. Now, these elite and secretive troops, their actions long shielded from public scrutiny, are the focus of a high-profile investigation that could shed unprecedented light on their methods and tactics. American and Afghan officials are probing a possible attempted coverup in the deaths of five Afghan civilians in February in a raid carried out by U.S. Special Forces accompanied by Afghan troops. Three of those killed were women and among the charges is that the bodies were tampered with by coalition forces to conceal the cause of death. The U.S. military this week accepted responsibility for the Feb. 12 slayings, initially blamed on insurgents, and on Thursday, senior officials met with family members of the slain civilians to offer an apology. But U.S. officials say allegations that bullets were dug out of the bodies as part of a coverup are baseless. A new investigation has been opened, military officials in Afghanistan said Thursday, to further look into the differences between findings by Afghanistan's Interior Ministry and an initial American inquiry, which remains classified. Special Forces are inextricably linked to one of the most contentious issues between the Afghan government and Western forces: civilian deaths and injuries. Special Forces account for a disproportionate share of civilian casualties caused by Western troops, military officials and human rights groups say, though there are no precise figures because so many of their missions are deemed secret. U.S. Army Gen. Stanley A. McChrystal, who took command of Western forces in Afghanistan last summer, has said such casualties are highly damaging to the Western effort, because they galvanize opposition to the foreign troop presence and fuel support for the insurgency. McChrystal last year instituted strict new rules of engagement meant to limit civilian casualties. But even under the new rules, Special Forces members, who have the task of hunting down key Taliban figures, continue to have more operational leeway than other troops. In mountain villages and desert hamlets, the Special Forces inspire dread among Afghans, who tend to speak of them in whispers. Their strikes are usually swift and violent, most often taking place in the dead of night. At Western military bases, Special Forces troops are readily identifiable by shaggy beards, vaguely Afghan-looking dress, preternaturally fit physiques and a forbidding manner. Usually housed in separate compounds, they rarely mix with other troops and tend to react explosively if anyone snaps a photo that might show their faces. Initial military accounts of the February raid in the Gardez district of Paktia province made it sound as if it were a successful instance of Western raiders swooping down on wanted militants. The North Atlantic Treaty Organization at the time described the slain men as armed insurgents who fired on coalition troops and said the women were already dead when the Special Forces arrived. But in the ensuing two months, the narrative changed dramatically. The slain men turned out to be an Afghan police official and a district prosecutor, according to local leaders. They identified the others as a teenage girl and two pregnant women whose deaths left motherless a total of 16 children. "We deeply regret the outcome of this operation, accept responsibility for our actions that night, and know that this loss will be felt forever by the families," said Canadian Brig. Gen. Eric Tremblay, a spokesman for the NATO-led International Security Assistance Force. Both U.S. and Afghan officials say questions remain about whether the scene of the raid -- a family compound in the village of Khatabeh -- was tampered with afterward in an effort to conceal the circumstances of the deaths. "By the time we got there, there was a foreign guy guarding the bodies, and they wouldn't let us come near," said Gen. Azizdin Wardak, chief of police in Paktia. Both the Interior Ministry and the U.S. military, under NATO's auspices, are investigating reports that coalition forces washed down the compound, dug bullets from the walls and collected casings from the ground. Though such actions could be consistent with a coverup, they could also have represented a legitimate effort to reconstruct and record the night's events, military officials say. A British newspaper, the Times of London, cited an Afghan investigator as saying raiding forces may have tried to extract bullets from the bodies in an apparent attempt to conceal how they were killed. The report said the unidentified investigator interviewed a relative who described a coalition soldier standing over one of the bodies with a knife. U.S. Rear Adm. Gregory Smith, McChrystal's spokesman, said no forensic evidence or eyewitness testimony had been presented to support that account. Zemari Bashary, a spokesman for Afghanistan's Interior Ministry, declined to detail the Afghan investigators' findings, which he said would be released in coming days. Smith said NATO would issue a report on the raid's aftermath, though he said some details might remain classified. Even in the absence of any proven coverup, the incident was a highly damaging one -- especially since the military had initially suggested that the women had been killed execution-style by insurgents or in a so-called honor killing by their own relatives, not in the course of the raid itself. "Joint Force Operating in Gardez Makes Gruesome Discovery," read the headline of NATO's first news release about the incident. The Special Forces raiders also apparently mistook a large celebration taking place in the compound for a gathering of insurgents. Shortly after the raid, McChrystal, a former high-ranking special ops commander, moved to assert control over Special Forces units operating here. Previously, many had separate chains of command. He also moved this year to limit night raids, a prime weapon in the Special Forces arsenal, because of the heightened risk of confusion and mistaken identity. In rural Afghanistan, most family compounds contain weaponry of some kind, increasing the likelihood that any accidental confrontation will take a lethal turn. Upon hearing gunshots outside at night, men will almost invariably grab a gun and try to defend themselves, drawing the raiders' retaliatory fire. Moreover, in this complex tribal society, Afghans sometimes try to settle clan feuds and other rivalries by fingering the other side as insurgents, as a means of bringing deadly raids down on the heads of their enemies. A notorious Special Forces-ordered nighttime airstrike in Azizabad in August 2008, which killed up to 90 people, was reported to have been prompted by a deliberately false tip about insurgent activity that reached the ears of the Western coalition. Most of the dead were civilians, according to the United Nations and the International Committee of the Red Cross. Special Forces are regarded with mistrust not only by many Afghans, but also by some in the conventional ranks of the Western military. Coalition field commanders responsible for operations in a given area often are not even aware of that a Special Forces strike is planned or taking place in their territory, but are left to deal with the consequences. In the southern province of Oruzgan, an airstrike in late February that was reportedly called in by Special Forces killed at least 27 people when their vehicles were mistaken for an insurgent convoy. Dutch troops operating in the area, who are acknowledged to be among the coalition's best at developing good relations with Afghan villagers, said they were not consulted, and said the raid was a serious setback to their efforts to win residents' trust. In Khatabeh, residents' anger remained palpable despite the high-level apologies, local leaders said. "People are still very, very upset," said Jannat Khan, a provincial council member from Gardez. "The Special Forces do these operations without telling anyone. And they don't know who is the enemy and who isn't." (latimes)