However, Major-General Michael Dunleavy denied that detainees were tortured, saying that he treated them "as human beings, but not like soldiers".
The documents do, however, detail the use of controversial interrogation techniques by US officers, such as disrupting sleep patterns, exploiting phobias and issuing verbal threats.
Clara Gutteridge from Reprieve International, an organisation campaigning for the fair treatment of prisoners, said the documents confirmed previous knowledge about the "systematic nature of abuse at Guantanamo Bay".
"[They] also document some of the abusive techniques that the United States does not consider torture but that everywhere else does consider torture," she told Al Jazeera.
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"One thing that is striking about the documents is that so much has been redacted from them; there are pages and pages that we can't read"
Clara Gutteridge,
Reprieve International
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"One thing that is striking about the documents is that so much has been redacted from them; there are pages and pages that we can't read.
"Presumably, what is underneath those pages is information about things that we do not know about.
"That raises a real question about [US president Barack] Obama's policy in relation to transparency about what has gone on in the past."
Dunleavy also reported that there was a lack of security and control over detainees when he arrived, according to one of the documents.
He said those being held at the camp would often riot and throw food, and turned spoons, welding rods and other items into weapons.
A staff attorney with the American Civil Liberties Union (ACLU), which filed the suit to have the 12 documents released, said that the situation in the camp should now be officially investigated.
"These documents ... further underscore the need for a congressional select committee to examine the roots of the torture programme as well as an independent prosecutor to investigate issues of criminal responsibility," Amrit Singh said.
Obama has ordered that the Guantanamo Bay facility, which still holds more than 200 prisoners, be closed next year.