The Bush administration met logistical and diplomatic difficulties in transferring prisoners held at the secretive Bagram Theater Internment Facility to a refurbished maximum security detention center controlled by the Afghan military, The New York Times (NYSE:NYT) reported Monday.

The difficulties concerned assurances from the government of Afghanistan regarding the treatment of and accountability for the prisoners transferred to Afghan custody.

The Afghan government rejected adopting a prison system modeled after the contentious U.S. naval detention center at Guantanamo Bay, Cuba, and the "enemy combatant" legal framework.

The diplomatic row comes as Pentagon and Red Cross officials expressed concerns about the treatment of detainees at the Bagram facility.

A confidential Red Cross memorandum said prison officials held many of its detainees in isolation for months in undisclosed wards and occasionally subjected them to cruel treatment in violation of humanitarian law, the Times said.