U.S. Waited Months to Book C.I.A. Prisoners at Guantánamo Bay

No explanation was offered for the delay, although the detainee processing took place after President George W. Bush announced on Sept. 6, 2006, that the prisoners were at Guantánamo. One reason for the disclosure, he said, was that “to start the process for bringing them to trial, we must bring them into the open.” Mr. Nashiri was arraigned in 2011, and the case has been repeatedly stalled through higher court challenges.

Several law enforcement agents on Monday described how, during their assignment to the Criminal Investigation Task Force, a prosecution support organization created by the Defense Department, they undertook the collection process on Nov. 30, 2006, in their first encounter with the former C.I.A. detainees. The agents operated what Mr. Miller called an “assembly line” to photograph, fingerprint and take DNA samples of each of the 14 prisoners, who were shackled at the wrists and ankles and guided through the process by two guards.

None of the men protested, complained or mentioned mistreatment, said Chief Warrant Officer Leona Mansapit of the Army. A military police soldier at the time, she took fingerprints from some of the prisoners. “It was very routine,” she said, aside from the late hour.

An investigator who took part in the processing, George E. Boyles, who had served in law enforcement and military roles since the late 1980s, said that evening at Guantánamo Bay was the only occasion in his career that he had taken what was essentially booking samples of suspects in their fourth year in custody.

Capt. Brian L. Mizer of the Navy, a military defense lawyer for Mr. Nashiri, accused the prosecutors of advancing “a sham argument that this was a routine booking procedure happening three months after they got here and four years after they came into U.S. custody.” Such procedures are done at the time of an arrest, Mr. Nashiri’s lawyers said, to confirm an identity or check for arrest warrants.

“I really don’t know where they were at before I saw them on Guantánamo Bay,” said Sheldon J. Beddo, a Naval Criminal Investigative Service agent who was based there in 2006 and oversaw the evidence collection at “a location I was not familiar with” made up of prefabricated buildings.

The question of who was in control of the detainees at Guantánamo Bay during that period has been in dispute for years. In 2014, a Senate Intelligence Committee study not only disclosed that there had been two C.I.A. black sites at the Navy base but also described Camp 7, the prison where Mr. Nashiri, Mr. Mohammed and other high-value detainees were held, as under the operational control of the C.I.A. during their first months at Guantánamo.

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