“GUANTÁNAMO BAY, Cuba — In the torturous history of the U.S. government’s black sites, the F.B.I. has long been portrayed as acting with a strong moral compass. Its agents, disgusted with the violence they saw at a secret C.I.A. prison in Thailand, walked out, enabling the bureau to later deploy “clean teams” untainted by torture to interrogate the five men accused of conspiring in the attacks of Sept. 11, 2001.
But new information that emerged this week in the Sept. 11 case undermines that F.B.I. narrative. The two intelligence agencies secretly arranged for nine F.B.I. agents to temporarily become C.I.A. operatives in the overseas prison network where the spy agency used torture to interrogate its prisoners.
The once-secret program came to light in pretrial proceedings in the death penalty case. The proceedings are currently examining whether the accused mastermind of the Sept. 11 plot, Khalid Shaikh Mohammed, and his four co-defendants voluntarily confessed after years in the black site network, where detainees were waterboarded, beaten, deprived of sleep and isolated to train them to comply with their captors’ wishes.
At issue is whether the military judge will exclude from the eventual trial the testimony of F.B.I. agents who questioned the defendants in 2007 at Guantánamo and also forbid the use of reports that the agents wrote about each man’s account of his role in the hijacking conspiracy.
A veteran Guantánamo prosecutor, Jeffrey D. Groharing, has called the F.B.I. interrogations “the most critical evidence in this case.” Defense lawyers argue that the interrogations were tainted by the years of torture by U.S. government agents.
In open court on Thursday, another prosecutor, Clayton G. Trivett Jr., confirmed the unusual arrangement, in which nine F.B.I. agents were “formally detailed” to the agency “and thus became a member of the C.I.A. and worked within C.I.A. channels.”
He said that the agents served as “debriefers,” a C.I.A. term for interrogators, and questioned black site prisoners “out of the coercive environment” and after the use of “E.I.T.s.”
E.I.T.s, or enhanced interrogation techniques, is a C.I.A. euphemism for a series of abusive tactics that the agency used against Mr. Mohammed and other prisoners in 2002 and 2003 — tactics that were then approved but are now illegal. They include waterboarding, painful shackling and isolating a prisoner nude, shivering and in the dark to break his will to resist interrogation.
Mr. Trivett offered no precise time period but made clear that the F.B.I. agents were absorbed by the C.I.A. sometime between 2002, when the black sites were established, and September 2006. On their return to the F.B.I., they took on the status of C.I.A. assets, he said, and so their identities are classified.