This article was produced in partnership with the Pulitzer Center on Crisis Reporting.

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.