The newspaper said Sunday the situation could affect President Barack Obama's plan to determine the fates of the detainees. Information on individual prisoners is "scattered throughout the executive branch," an Obama administration official said.
The Post said the executive order Obama signed Thursday requires the detention center to be closed within a year and creates a cabinet-level panel to review each case separately, but the efforts could be hampered by the lack of case files.
Charles "Cully" Stimson, who served as deputy assistant defense secretary for detainee affairs in 2006 and 2007, said he had persistent problems in attempts to assemble information on individual cases.
Pentagon spokesman Geoff Morrell said the Defense Department would cooperate fully in the individual case reviews.
"Fundamentally, we believe that the individual files on each detainee are comprehensive and sufficiently organized," Morrell said. He added that "in many cases, there will be thousands of pages of documents ... which makes a comprehensive assessment a time-consuming endeavor."