The documents were released on the FBI's website and were turned over to the American Civil Liberties Union as part of its lawsuit.
"The idea that this is new is misguided and misleading"
Bryan Whitman, US Defence Department spokesman
Many of the incidents in the documents have already been reported and are summarised in the ACLU's lawsuit, though the report notes some smaller details about some of the incidents that are new.
The records were gathered as part of an internal FBI survey in 2004 that questioned 500 FBI employees about treatment of prisoners at the US military base in Cuba.
Bryan Whitman, a defence department spokesman said: "The idea that this is new is misguided and misleading.
"These are things the department has thoroughly investigated and where allegations have been substantiated, disciplinary action has been taken."
Asked if the Pentagon plans any follow-up to the report, Whitman said: "No, it's already been thoroughly investigated."
The Pentagon has said the population of the prison now stands at approximately 395 inmates. Most were captured during the US-led invasion of Afghanistan after the September 11 attacks.