The U.S. flag is seen at the U.S. Naval Base in Guantanamo Bay, Cuba. (CHANTAL VALERY/AFP/Getty Images)

A psychologist who examined one of the defendants on trial at Guantanamo Bay, Cuba, in connection with the terrorist attacks of Sept. 11, 2001, concluded that the high-value detainee was mentally incompetent, raising questions about his fitness to stand trial, according to individuals familiar with the finding.

For three days in January 2009, Xavier Amador, a professor at Columbia University, interviewed Ramzi Binalshibh, an al-Qaeda operative and protege of alleged Sept. 11 co-conspirator Khalid Sheik Mohammed. He determined that Binalshibh didn’t understand the proceedings against him and suffered from delusions, said one of the individuals who has reviewed the case.

Amador’s assessment, which has not been known publicly until now, comes as the military commission case against Binalshibh, 41, has stalled over questions about his mental health and whether he is fit to stand trial with four other suspected al-Qaeda members, including Mohammed. He was held for years at secret CIA prisons, where he was subjected to “enhanced interrogation techniques” that human rights advocates have described as torture.

The psychologist’s conclusion could presage a similar finding by a medical review board that was ordered by a judge last week to evaluate Binalshibh. Such a determination could cast into doubt the prosecution of one of the key defendants in the Sept. 11 attacks.

The individuals familiar with Binalshibh’s case spoke on the condition of anonymity because details are being kept under protective order from the court at Guantanamo Bay.

Ramzi Binalshibh is seen in a photo released January 17, 2002. (HANDOUT/REUTERS)

Prosecutors previously told the court that Binalshibh suffered mental health problems and was taking a variety of medications for “schizophrenia and/or bipolar disorder,” but the military commission at Guantanamo Bay has never come to a determination about his fitness to stand trial.

Binalshibh is accused of playing a key role in the Sept. 11 conspiracy. According to the 9/11 Commission report, he provided assistance to the hijackers and colluded with ringleader Mohamed Atta, who piloted American Airlines Flight 11 into the North Tower of the World Trade Center. Binalshibh, the report found, sought to participate in the attacks but was unable to get a U.S. visa.

Last week, a military judge ordered a medical board to evaluate Binalshibh after the detainee was repeatedly thrown out of the courtroom during proceedings because of erratic behavior.

Binalshibh has been given a diagnosis of persecutory delusional disorder, but prosecutors said in their most recent court filing that psychiatrists who examined him in the past thought he was fit to stand trial. Prosecutors did not mention Amador’s finding, but court records indicate that he spoke with Binalshibh in 2009 as part of a hearing to determine whether Binalshibh could challenge his detainment in federal court.

Binalshibh refused to cooperate with a 2008 order that he be examined by a medical board. The issue was never resolved because the case was put on hold after President Obama took office in 2009 and halted the tribunals at Guantanamo. Charges against detainees were later refiled.

The issue of Binalshibh’s fitness to stand trial resurfaced after prosecutors requested that doctors examine him. The move was unusual because it is usually defense lawyers who make such a request; in Binalshibh’s case, prosecutors probably need to address the issue to avoid the chance that a conviction could be overturned.

One of Binalshibh’s previous defense lawyers has said the Yemeni’s time in CIA custody appears to have contributed to his mental health problems. People familiar with the case say he was angered when those lawyers raised questions about his sanity, possibly explaining why his current counsel has not.

Binalshibh spent four years in CIA custody, beginning in September 2002. He languished in prolonged isolation in “black sites” in Poland, Morocco and Romania. He could be defiant and petulant, according to former CIA officials.

In the secret prisons, detainees were exposed to interrogation techniques that were “designed to psychologically ‘dislocate’ the detainee, maximizing his feeling of vulnerability and helplessness, and reduce or eliminate his will to resist,” the CIA inspector general’s report on the program said.

By the time Binalshibh landed at Guantanamo Bay in 2006, he was having problems, according to a 2009 unredacted court document obtained by The Washington Post.

A U.S. Navy psychiatrist examined him shortly after he was transferred to the prison and found he had an “Adjustment Disorder with Depressed Mood.” In a follow-up visit with Binalshibh the next month, the doctor reported that the detainee could not sleep “day or night” because of problems he suffered at another facility and that he complained about “noises, odors, and slight vibrations.”

By January 2007, his condition had worsened, and the same doctor submitted a memorandum requesting that Binalshibh be given anti-psychotic medication without his consent.

The memorandum said Binalshibh had a “history of fixed, firm, false beliefs” and “as a result of his delusional beliefs, the detainee becomes irritable, angry, and agitated episodically, which has resulted in two Forced Cell Extractions this month.”

The Navy doctor said Binalshibh had a delusional disorder for which he has “no insight,” meaning he might not have known he was mentally ill.

Binalshibh’s lawyer, James Harrington, said Amador’s 2009 opinion has no bearing on the case today because Amador never testified and his findings were never admitted into the court record.

Amador, a clinical and forensic psychologist, once examined Zacarias Moussaoui, the only person convicted in a U.S. court in connection with the Sept. 11 attacks. In 2006, he testified in the Moussaoui case that “of about 30 cases I have worked on, I find people competent in the overwhelming majority of those cases. I have only found people incompetent four times.”

Jury selection in the case of Binalshibh and the other Sept. 11 co-conspirators could begin in January 2015, but it has been delayed repeatedly in the past.