Attorney James Harrington told the judge presiding over the case at the Guantanamo Bay naval base that the agents asked about activities of others on his defense team as well as of people working for other defendants.
"Obviously, to say that this is a chilling experience for all of us is a gross understatement," he told the judge.
The defense security officer, a private contractor who assists with the handling of classified material in the death-penalty terrorism trial, was also asked to sign an agreement that implied he might be asked to provide information to the FBI on an ongoing basis in the future, Harrington said.
The questioning occurred April 6 at the man's home in the United States, not on the US base in Cuba.
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The lawyer said the apparent investigation of defense team members will require review by the court, and possibly the appointment of additional counsel for the defendants because it has created a potential conflict of interest for the attorneys.
"If we are the subject of some inquiry or investigation or whatever by the FBI or some other government agency, then we have an interest in how that comes out and the question becomes whose interest do we protect first, ours or our clients," he said.
He urged the judge to continue with the scheduled competency hearing, which had already delayed the long-stalled trial by military commission for five Guantanamo prisoners charged with planning and aiding the September 11 terrorist attack.