He said the detainees will be transferred to the United States after all legal requirements, including a 45-day notice and report to Congress are fulfilled, and after state and local authorities have been consulted. They will be housed in maximum-security units in New York that have held other terrorism suspects. Once federal charges are filed against the five men, military charges now pending against them will be withdrawn.

The prosecution of cases in both federal court and military commissions may be complicated by the treatment of detainees while in CIA custody. Both Mohammed and Nashiri were waterboarded at secret agency “black sites,” and defense lawyers are likely to press hard to get evidence of abuse into the court record. CIA interrogators also used a handgun and an electric drill in an attempt to frighten Nashiri into giving up information, according to a report by the CIA’s inspector general, portions of which were released earlier this year. Intelligences sources said the drill was held near Nashiri and turned on and off repeatedly, and the suspect was also shown a gun to make him believe he would be shot.