Attaullah Khogiani, a spokesperson for the governor of Wardak province, described a series of recent incidents of the alleged misconduct.
The first involved a university student who was visiting his relatives in a village for the holidays. According to Khogiani's account, which he says is based on witness reports, a joint team of U.S. and Afghan forces took the student from his home. Days later, the student's body was reportedly found under a bridge with torture marks and a slit throat.
In a second incident, a bus driver was shot, and in a third, nine villagers were rounded up and taken away by a joint team of U.S. and Afghan forces, never to be seen or heard from again. Khogiani said their whereabouts are still unknown.
"When we investigated further, we found that the Afghan forces behind this were not part of the Afghan National Army, the NDS [Afghanistan's intelligence agency], or any other department within Afghanistan's national forces," Khogiani said.
Khogiani said that when local officials realized the Afghans behind the disappearances were working directly under U.S. Special Forces – with no official Afghan oversight – they raised the issue with the country's National Security Council, which in turn dispatched a team to investigate. That team quickly verified the claims were true, Khogiani said.
Khogiani declined to name the villages or any local elders who could authenticate the accusations, saying they were afraid of reprisals.
Pentagon spokesperson Commander Bill Speaks declined to comment today on Khogiani's specific allegations except to say that ISAF is looking into them and similar claims made in the past were found to be unsubstantiated.
Regardless, many Afghan officials said the lack of clarity surrounding the shadowy campaign forces is unacceptable.
Still, the provinces that the U.S. Special Operations forces have been ordered to abandon are just outside of Kabul and are considered transit ways for militants to the south and east to enter the capital. The expulsion has already raised concerns of more terrorist attacks in Kabul, particularly with the annual summer fighting season set to begin.
ABC News' Lee Ferran contributed reporting from New York.