WASHINGTON » In April 2001, seven months after the Navy destroyer Cole was bombed in Yemen, Abd al-Rahim al-Nashiri was staying at a Qaida guesthouse in Afghanistan where he is alleged to have laid out how he had planned the whole thing.

One of those houseguests was later captured, and he told FBI agents the story of those boasts and implied that he could be a star witness if Nashiri were tried for the murder of the 17 American sailors killed in the attack.

That trial is going to happen, but that witness is no longer available. Still, prosecutors may not need him. Nashiri will be tried by a military commission, and under the rules there, FBI agents can simply repeat the accounts of witnesses—indirect testimony that would generally be inadmissible in a civilian court.

Nashiri's case will be the marquee test of a new tribunal system designed to handle suspected terrorists. But the decision by Attorney General Eric H. Holder Jr. to prosecute him before a commission, while putting the self-proclaimed mastermind of the Sept. 11 attacks, Khalid Shaikh Mohammad, before a civilian court, has set off a fierce debate.

Some conservatives have argued that all accused terrorists should be tried before commissions, like the one that will decide Nashiri's fate. It is too risky, they contend, to try any terror defendant in the civilian legal system, where the rules of evidence are far more restrictive.

Civil libertarians, on the other hand, contend that the administration's approach amounts to a two-tier system in which cases with weaker evidence receive second-class justice by being shunted into the looser commission system.

A close look at the evidence against Nashiri provides a case study of the significant differences that remain between civilian trials and military commissions, even after a recent overhaul by Congress. It shows that it would indeed be simpler to introduce certain evidence against terror defendants in commissions, but that nagging questions about the legality of the military court system present significant hurdles.

A review of public documents and interviews with current and former officials familiar with the case also illuminates the difficult trade-offs the administration faces as it pores through the prison population at Guantanamo Bay, Cuba, and decides the fates of detainees like Mohammad and Nashiri.

In explaining why Nashiri would not receive a civilian trial, Holder cited “;a variety of factors”; while emphasizing one in particular: It “;was an attack on a United States warship, and that, I think, is appropriately placed into the military commissions setting.”;

But several current and former officials familiar with the case say that concerns about the evidence against Nashiri were an overriding factor. Prosecuting him under the more stringent rules of civilian court would have been perilous. Most of that evidence consists of hearsay—statements made outside court, like the former detainee's account of what he said he heard Nashiri say in April 2001.

In a civilian trial, hearsay statements generally cannot be introduced because there is no opportunity for defense lawyers to cross-examine the witness. But under commission rules, FBI agents could tell a military jury what Nashiri told the detainee, according to the detainee.

“;In a federal court where the Constitution applies, a defendant is allowed to confront his accusers face to face,”; said Lt. Cmdr. Stephen Reyes of the Navy, the military lawyer assigned to represent Nashiri. “;In this case, Nashiri could be convicted and put to death without ever seeing any one of his accusers take the stand.”;

But Bryan Whitman, a Pentagon spokesman, said the government's case that Nashiri was al-Qaida's key organizer of the Cole attack was solid, and characterized the legal protections available to the defendant as “;unprecedented in the history of modern warfare.”;

“;The fact that many of the potential witnesses are citizens of other nations who cannot be compelled to attend trial in the United States is one of several evidentiary concerns that make trial by military commissions the proper legal venue,”; Whitman said.

The case against Nashiri also includes some evidence the defense is likely to portray as circumstantial: business records with his name or aliases related to the renting of safe houses and the registration of cars used in the operation, as well as the purchase of the small boat on which two suicide-bombers carried the explosives to the side of the Cole while it was refueling in the harbor next to Aden, Yemen, on Oct. 12, 2000.

But unlike Mohammed, who has repeatedly admitted planning the Sept. 11 attacks, Nashiri, who was apparently in Afghanistan at the time of the Cole attack, is expected to strongly deny plotting to bomb the warship. While he admitted taking money from Osama bin Laden to buy the boat in a March 2007 military hearing at Guantanamo, he claimed he intended only to start a fishing business.

According to a hearing transcript, Nashiri claimed that when he later learned that Bin Laden was interested in using that boat for an attack, he wanted no part of it and left Yemen without knowledge of any specific plan. He also claimed that one of the attackers had used his name and identification card for the business paperwork without his knowledge or permission.

“;I had nothing to do with this bombing,”; Nashiri said, adding: “;We were planning to be involved in a fishing project. I left the thing; I left the project and left. They are the ones who were involved in those things. I'm not responsible for them or what they have in their heads.”;

In a civilian trial, that circumstantial evidence and Nashiri's denials could be virtually all that jurors would have to consider when deciding his guilt or innocence beyond a reasonable doubt.

But jurors in a commission trial—handpicked by a senior Pentagon official—would learn much more about the government's contention that Nashiri was the architect of a bombing that gripped the nation.

Court and military documents show that the FBI has turned up other information that would significantly strengthen its case against Nashiri, evidence that could be used in a commission trial but not in civilian court.

First, there is the account of Nashiri's boasts at the Qaida guesthouse in April 2001. That story came from Salim Hamdan, a former driver for Bin Laden who was the plaintiff in the 2006 Supreme Court case striking down the first form of President George W. Bush's military commissions.

Hamdan, who spent seven years in Guantanamo, is free in Yemen and cannot be forced by the United States to appear.

Other evidence accumulated by the FBI agent who led the Cole investigation, Ali H. Soufan, includes interviews with several other witnesses in Yemen, among them two men suspected of being co-conspirators who are alleged to have identified Nashiri as the organizer of the plot. Both men have been indicted by the United States, but Yemen has refused to extradite them. Soufan, who has since left the FBI, could testify in their absence about the substance of their interviews.

In addition, according to a footnote in the 9/11 commission report, in December 2001, a detainee told an interrogator that “;9/11 hijacker Khalid al-Mihdhar told him about the maritime operation sometime in late 1999 and credited Nashiri as its originator.”;

FBI agents also gathered other hearsay material that they say connects Nashiri to al-Qaida more generally, evidence that could also be presented more easily in a commission trial.

Still, some evidence in the Nashiri file could not be admitted no matter where he is prosecuted.

Under the recently revised military commission rules, information obtained by torture or other forms of cruel, inhuman or degrading treatment may not be used as evidence.

That means that accounts of Nashiri's role given by some detainees under interrogation by the CIA—including Mohammed and another man facing a civilian trial for the Sept. 11 attacks, Walid Bin Attash—would likely not be admissible.

Similarly, Nashiri himself initially confessed to the CIA that he had orchestrated the Cole attack. But that would probably not be deemed admissible because he later recanted and said that he had made it up under torture.

CIA interrogators subjected Nashiri to waterboarding, a technique that simulates drowning approved by Bush officials. Moreover, the CIA inspector general determined that Nashiri's was the “;most significant”; case of a detainee's being brutalized in unauthorized ways, including being threatened with a power drill and a handgun.

But the relative flexibility of the commission system could also prove to be its undoing.

Defense lawyers are expected to argue that terror defendants are entitled to the same protections as everyone else, particularly when it comes to challenging all witnesses face to face. The Sixth Amendment of the Constitution entitles a defendant “;to be confronted with the witnesses against him.”; As recently as 2004, the Supreme Court unanimously reversed a conviction because a judge had allowed hearsay evidence to be introduced by a police officer who had investigated the crime.

Several other unresolved legal clouds also hang over the commissions, and it could take years for the Supreme Court to resolve them, potentially delaying commission trials or calling into question any guilty verdict that results from them—another reason the administration has decided that when prosecution of a detainee is feasible, it will usually do so in the civilian courts.

Nashiri's military lawyer has already filed a lawsuit in the U.S. Court of Appeals for the District of Columbia challenging the system and asking the courts to stop any effort to prosecute his client before the commission.