Fernando Campoamor-Sanchez, a senior Justice Department official, said the FBI did not use an informant or other source working undercover to infiltrate the five defense teams, as defense lawyers have said.
He urged the judge, Army Col. James L. Pohl, to disregard defense motions to put FBI agents on the witness stand to determine whether they had spied on defense teams and violated their defendants' rights.
Although he provided few details in open court, Campoamor-Sanchez said the FBI agents had looked into "personnel security clearance" issues of several defense team associates, including those representing
The FBI apparently sought to determine whether anyone illegally forwarded confidential and classified material, including leaking a written manifesto from Mohammed to the outside world. In it, he said he now believes violence is forbidden by the Koran and that he hopes to convert his captors to Islam.
Campoamor-Sanchez indicated that the operation began in January 2013 and was closed May 12. He did not say whether the FBI found any illegal leaking, but he asked the court not to investigate any further.
"It is done," he said.
The secret inquiry surfaced in April when defense lawyers at Guantanamo Bay advised the judge that two FBI agents had approached a defense aide for one of the defendants, Ramzi Binalshibh, at his home in northern Virginia on a Sunday.
The FBI agents asked the aide about the inner workings of the defense operation, and urged him to sign a nondisclosure statement as a confidential FBI informant, the judge was told. The aide refused.
Federal agents made similar approaches to at least three other defense assistants, the court was told Monday.
The question of whether the FBI acted inappropriately has forced a halt to the prosecution of the five Sept. 11 defendants. Defense lawyers have asked Pohl to order a separate evidentiary hearing to determine whether the defense teams were compromised.
David Nevin, the lead attorney for Mohammed, told the judge Monday that he would consider withdrawing from the case if Pohl did not convene the evidentiary hearing. He said he had canceled a fact-finding trip to the Middle East for fear that government agents would shadow him.
"I believe we're under scrutiny all of the time," Nevin said.
Walter Ruiz, the lead attorney for Mustafa Ahmed Hawsawi, asked the judge to separate his case from the other defendants, saying the taint of misconduct could harm his client.
James Harrington, the lead attorney for Binalshibh, complained that the government had compromised his defense squad by recruiting an aide as an informant.
"We have had basically a spy within our team for a number of months," he said. "It is certainly very troubling to us."
The judge said he would announce later whether to hold the evidentiary hearing.
The battle over the FBI's involvement is the latest delay in the case that, if it ever goes to trial, would be the first and probably only prosecution of anyone directly involved in the Sept. 11, 2001, terrorist attacks.
The five defendants were captured a dozen years ago and arraigned two years ago. Since then, the case has bogged down in pretrial hearings and other legal matters.
Brig. Gen. Mark Martins, the lead military prosecutor, insisted outside the courtroom that the case was moving forward. He said more than 293,000 pages of unclassified material had been given to each of the defense teams, 154 legal motions had been filed and argued, and 22 witnesses had given testimony. In addition, he said, 190 exhibits have been filed.
He also acknowledged that "much remains to be done," and that "as we continue to move toward trial, the passage of time will not diminish our resolve."
Critics view the long delays as evidence that the military tribunals used at Guantanamo Bay do not work, and argue that the accused terrorists could have been tried and convicted in civilian courts years ago.
All five defendants have pleaded not guilty. The hearings at Guantanamo Bay are simulcast at