WASHINGTON (AP) — A U.S. military officer warned Pentagon officials that an American detainee was being driven nearly insane by months of punishing isolation and sensory deprivation in a U.S. military brig, according to documents obtained by The Associated Press.

While the treatment of prisoners at detention facilities at Guantanamo Bay, Cuba, and in Afghanistan and Iraq have long been the subject of human rights complaints and court scrutiny, the documents shed new light on how two American citizens and a legal U.S. resident were treated in military jails inside the United States.

The Bush administration ordered the men to be held in military jails as ‘‘enemy combatants’’ for years of interrogations without criminal charges, which would not have been allowed in civilian jails.

The men were interrogated by the CIA and Defense Intelligence Agency, repeatedly denied access to attorneys and mail from home and contact with anyone other than guards and their interrogators. They were deprived of natural light for months and for years were forbidden even minor distractions such as a soccer ball or a dictionary.

‘‘I will continue to do what I can to help this individual maintain his sanity, but in my opinion we’re working with borrowed time,’’ an unidentified Navy brig official wrote of prisoner Yaser Esam Hamdi in 2002. ‘‘I would like to have some form of an incentive program in place to reward him for his continued good behavior, but more so, to keep him from whacking out on me.’’

Yale Law School’s Lowenstein International Human Rights Clinic received the documents through a Freedom of Information Act request filed by two attorneys Jonathan Freiman and Tahlia Townsend, representing another detainee, Jose Padilla. The Lowenstein group and the American Civil Liberties Union said the papers were evidence that the Bush administration violated the 5th Amendment’s protections against cruel treatment. The U.S. military was ordered to treat the American prisoners the same way prisoners at Guantanamo were treated, according to the documents.

However, the Guantanamo jail was created by the Bush administration specifically to avoid allowing detainees any constitutional rights. Administration lawyers contended the Constitution did not apply outside the country.

‘‘These documents are the first clear confirmation of what we’ve suspected all along, that the brig was run as a prison beyond the law. There was an effort to create a Gitmo inside the United States,’’ Jonathan Hafetz of the ACLU’s National Security Project in New York said, using the slang word for the U.S. naval facility in Cuba.

The 91 pages of e-mails and documents produced by U.S. Fleet Forces Command, which runs the military brigs in Norfolk, Va., and Charleston, S.C., detail daily decisions made about the treatment of Hamdi and Padilla, then both American citizens, and Ali Saleh Kahlah al-Marri, a legal resident. All were designated as by the White House as ‘‘illegal enemy combatants.’’

The paperwork show uniformed officials at the military brigs growing increasingly uncomfortable and then alarmed that they were being directed to handle their prisoners under the rules that governed Guantanamo.

The authors and recipients of the e-mails are censored from the documents. They appear to be going to either military or Pentagon legal counsel and policy offices.

The documents show that some officials at the Charleston brig were deeply skeptical about the mandate that Guantanamo rules should apply in the United States, a decision made by the defense secretary’s office, according to the documents.

‘‘You have every right to question the ’lash-up’ between GTMO and Charleston — it was the first thing I ask (sic) about a year ago when I checked on board,’’ wrote one official to another in 2006. ‘‘In a nutshell, they gave the Charleston detainee mission to (Joint Forces Command) who promptly gave it to (Fleet Forces Command) with a ’lots of luck’ and nothing else.’’

An officer was still raising alarms about Hamdi’s mental state after 14 months of jail with no contact with lawyers, his family or even other prisoners.

‘‘I told him the last thing that I wanted to have happen was to send him anywhere from here as a ’basket case,’ of use to no one, to include himself,’’ the officer wrote in an e-mail to undisclosed government officials in June 2003. ‘‘I fear the rubber band is nearing its breaking point here and not totally confident I can keep his head in the game much longer.’’

The frustrated officer wrote that he had ‘‘to have the ability to exercise some discretion when I believe it best for the health and welfare of those assigned to my facility … Know … we are to remain consistent with the procedures that were/are in place at Camp X-Ray’’ a reference to the Guantanamo jail. He pointed out that imposing those conditions in the brig had a far harsher effect on his prisoners because they had no contact with any other detainees, which was allowed at Guantanamo.

Scores of pages of once-secret legal opinions regarding detainee rights and treatment have been released under the Freedom of Information Act. At least two apparently crucial memos about enemy combatant treatment inside the U.S. have yet to be made public.

Hamdi was captured in Afghanistan in 2001, shipped to Guantanamo and then moved to the U.S. after his citizenship was discovered. He was held and interrogated for three years without charges. The Supreme Court in 2004 rejected the government’s attempt to hold him indefinitely without charge. He was released to Saudi Arabia on the condition he give up his U.S. citizenship.

Al-Marri, a citizen of Qatar, was a legal resident studying for a master’s degree in Illinois when he was arrested in December 2001 by the FBI as a material witness to the Sept. 11, 2001, attacks. He was charged with credit card fraud in 2002. A month before his trial in 2003, President Bush declared him an enemy combatant and al-Marri was transferred to the consolidated naval brig in Charleston. There he was held in isolation for 16 months, denied shoes and socks for two years, and was not allowed any contact with his family for five years. He remains in the military brig but is appealing his detention to the Supreme Court.

Padilla was arrested in 2002 under suspicion he was collaborating with al-Qaida to build a radioactive or ‘‘dirty’’ bomb. He was held as an enemy combatant for more than three years. He was held totally incommunicado for 21 months. His mother was only allowed to see Padilla after she agreed not to alert the media to the visit, according to the documents.

The government dropped the dirty bomb charges and Padilla’s case was moved to civilian court where in 2007 he was convicted of supporting terrorism in Kosovo, Bosnia and Chechnya.