GUANTÁNAMO BAY, Cuba — An F.B.I. agent testified in a pretrial hearing in the Sept. 11, 2001, conspiracy case on Thursday that he sent hundreds of questions into the secret prison network where the C.I.A. used torture to interrogate its prisoners, a collaboration that the bureau has never acknowledged.
The testimony appeared to contradict earlier suggestions from the F.B.I. that it had distanced itself from the interrogation program.
And it appeared to help the case being made by defense lawyers that the judge should exclude interrogations by the F.B.I. of the five men accused of plotting the Sept. 11 attacks. F.B.I. agents interrogated the men at Guantánamo in 2007, months after the prisoners were transferred out of the C.I.A. program. The defense lawyers argue that the F.B.I. interrogations were tainted by the torture as well as an F.B.I. role in the black sites.
James G. Connell III, a lawyer who represents one of the defendants, Ammar al-Baluchi, read aloud about 70 questions from hundreds that Special Agent James M. Fitzgerald sent to the C.I.A. in June 2003 to ask of the men now charged in the death-penalty case.
By then, C.I.A. agents had waterboarded the accused mastermind of the Sept. 11 attacks, Khalid Shaikh Mohammed, 183 times and interrogated him and his four co-defendants with other violence, sleep deprivation, dietary manipulation and rectal abuse. Prosecutors cannot use those 2002 to 2006 interrogations because the law that created the military commissions used to try the detainees requires that confessions must be voluntary.
In an effort to get confessions that would satisfy the law, the Defense and Justice Departments brought teams of F.B.I. agents to Guantánamo to question the defendants without threats, and without lawyers, in early 2007. The idea was that the new interrogators would get uncoerced, untainted confessions based on independent investigations of the Sept. 11 attacks.
The military judge, Col. W. Shane Cohen of the Air Force, has scheduled a trial date of Jan. 11, 2021. Between now and then he is holding on-again, off-again hearings on the defense lawyers’ bids to exclude the Guantánamo interrogations as tainted by torture.
Prosecutors have described the F.B.I.’s written accounts of those interrogations as crucial trial evidence.
Mr. Fitzgerald spent four days in 2007 questioning Mr. al-Baluchi at Guantánamo in a former C.I.A. black site called Camp Echo II. Mr. al-Baluchi admitted that he sent $119,500 in a series of money transfers to the hijackers in the United States, on behalf of his uncle, Mr. Mohammed. Mr. al-Baluchi’s lawyers have said he did not know how the money would be used.
Mr. Fitzgerald also showed him photos of the hijackers and had him identify them one by one.
In the written questions he sent in 2003 to the black sites, Mr. Fitzgerald sought details about a range of issues — including the travels of the 19 hijackers in the United States, financial transactions that led back to Mr. al-Baluchi and their foreign travel and overseas training.
Mr. Connell asked Mr. Fitzgerald if he knew, when he sent in the questions, that the defendants would be tortured. A case prosecutor, Jeffrey Groharing, objected to the word torture. So Mr. Connell rephrased his question.
“When you wanted the C.I.A. to ask these questions of their secret, incommunicado detainees, did you think they were going to ask nicely?” he asked.
“I wouldn’t use the word nicely, no,” Mr. Fitzgerald replied. “There were 3,000 dead people and there were a multitude of threats and unknown information. I considered the actions I took at that time to be reasonable.”
The agent said that by the time he interrogated former C.I.A. prisoners at Guantánamo in 2007, he knew generally about the “enhanced interrogation techniques” the agency used on the prisoners, but did not know about “their day to day life” or “what a black site was like."
In response to questions from the judge, Mr. Fitzgerald said he believed that a new location, new interrogators and questions that focused on identifying documents would separate the confessions he got from what the C.I.A. had extracted from the prisoners.
Mr. Fitzgerald testified this week that he and other agents who were assigned to investigate after the Sept. 11 attacks were able to read C.I.A. cables sharing intelligence from the black sites. But he testified that he never received a list of answers to his questions.
Then Mr. Connell showed the agent and the judge a series of classified cables outlining the information the C.I.A. had extracted from Mr. al-Baluchi — which contained answers to those questions — and Mr. Fitzgerald agreed that his 2007 Guantánamo interrogations got identical explanations.
He said he did not remember seeing those cables and could not recall if other F.B.I. agents who were privy to the cables pointed out the answers. Colonel Cohen, the judge, told the agent that it was likely that he saw the information in C.I.A. reporting. “I may have seen a cable,” Mr. Fitzgerald said. “I don’t have a specific recollection. I may have seen a cable that may have articulated something like that.”
But he said whatever cables he would have read from the black sites were to “generate intelligence” to stop further attacks.
Defense lawyers have asked the judge to exclude accounts of the F.B.I. interrogations as tainted by torture in several ways. They argue that the C.I.A. systematically broke the detainees so thoroughly that they gave F.B.I. agents involuntary, programmed responses drilled into them by their interrogators in the black sites. Moreover, they said the F.B.I. agents were compromised by their knowledge of the intelligence obtained by the C.I.A.
In a new disclosure, Mr. Connell announced in court last week that the F.B.I. had assigned agents to the black site program, a fact that the United States government declassified on the eve of the hearings. He also disclosed that, shortly after Mr. al-Baluchi was arrested in Karachi in 2003, an F.B.I. agent named James M. Fitzsimmons questioned him.
Mr. Fitzgerald said he believed that, when he interrogated Mr. al-Baluchi in Guantánamo in 2007, he was the first F.B.I. agent to question him. He said he had since learned that another agent questioned him as “part of a C.I.A. team” — upon which the court security officer hit a censorship button and court audio was masked by white noise.
Once the audio was restored, Mr. Connell said he would pose questions about that program in a classified session with only the judge, prosecutors and defense lawyers hearing the testimony. One was held Thursday evening. It was scheduled to continue Friday morning.