GUANTÁNAMO BAY, Cuba — At a hearing in the U.S.S. Cole bombing case this week, a retired F.B.I. agent described what three Yemeni eyewitnesses had told investigators 20 years ago after the suicide attack on the Navy warship.
According to the agent, the Yemenis pointed to a photo of Abd al-Rahim al-Nashiri, a Guantánamo prisoner now awaiting a death-penalty trial, as the person who had rented a safehouse used by plotters of the attack.
Confronted with the image on cross-examination, the former agent, Ammar Barghouty, said he was mistaken. The eyewitness had identified one of the suicide bombers, not Mr. Nashiri, as the tenant.
The rare “Law & Order” moment in the long-running case illustrated the challenge confronting the judge more than two decades after the Qaeda attack killed 17 American sailors and wounded dozens more in the port of Aden, Yemen, on Oct. 12, 2000.
Prosecutors contend they have no way of finding or bringing to Guantánamo the Yemeni men and boys whom U.S. agents questioned in the days, months and years after the attack. It is the judge’s job to decide in which instances mostly retired former agents can testify as stand-ins for about 100 missing witnesses.
The judge, Col. Lanny J. Acosta Jr., must determine in hearings now underway which of the hearsay statements, as they are called, are reliable enough to be presented to the military jury that will someday hear the death-penalty case.
The hearsay hearings began this summer and will continue into next year, with agents searching their memories to recall interviews in Yemen in the early 2000s. Prosecutors often hand the agents the accounts they wrote at the time to refresh their recollections.
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Testimony has shown that U.S. agents operated under such strict restrictions imposed after months of negotiations by the U.S. ambassador that, even if Yemen were not embroiled in civil warfare, many Yemeni witnesses would never be found.
For starters, Yemeni security forces located and brought the witnesses to the interviews, which were held at intelligence service compounds.
U.S. agents interviewed most witnesses just once, with Yemeni intelligence representatives always in the room, usually at the witnesses’ side.
Agents described an at-times hostile atmosphere. They were not allowed to canvass neighborhoods unescorted, nor were they able to photograph witnesses or obtain contact information to confirm their identity or to reach them later.
Part of the judge’s analysis involves why certain witnesses are unavailable. Two of the witnesses, whom U.S. interrogators questioned in a Yemeni prison, were subsequently killed in U.S. drone strikes.
Yemen is such a dangerous place that the ambassador works remotely. The U.S. Embassy there suspended operations in 2015. A year ago, Houthi forces broke into the compound and captured Yemeni employees of the United States or United Nations, a dozen of whom are still detained. One died in detention. The Pentagon prohibits war court personnel from traveling there.
Navy and F.B.I. agents have described arriving at the foundering, still burning wreck of the Cole, speaking to shocked survivors and then being stymied in their efforts to investigate onshore.
Yemeni security service members brought witnesses to the Americans with prepared statements based on Yemeni interrogations, which were read aloud before U.S. investigators could ask questions.
Agent Kenneth S. Reuwer of N.C.I.S., who questioned port workers in a room at a prison compound in February 2001, called the investigative conditions “extremely restrictive.”
Each witness sat five feet from the investigators. Mr. Reuwer said that he or an F.B.I. teammate would ask a question, without making eye contact with the witness, and a U.S. linguist would translate. Then the Yemenis would pose the question to the witness, sometimes after questioning the question. A Yemeni general was always in the room.
Pushing back against the process seemed unwise. The interviews could be ended “on the snap of a finger by the host country,” said Mr. Reuwer, who retired in 2014.
In court this week, his role was to describe interviews he conducted about three months after the attack with workers who heard an explosion and then looked into Aden harbor to see thick black smoke over the destroyer.
Another unavailable witness is Salim Hamdan, a former driver for Osama bin Laden in Afghanistan. Mr. Hamdan was convicted of war crimes at Guantánamo in 2008 and sent home, but ultimately acquitted four years later because of flawed charges in the case. Defense lawyers say he is unwilling to testify.
Prosecutors want a former federal agent to tell the military jury what Mr. Hamdan said during a pretrial interrogation: that before the bombing of the Cole, Mr. Hamdan saw Mr. Nashiri testing explosives in Kandahar, Afghanistan.
Defense lawyers have argued that Mr. Hamdan’s accounts should be excluded from the trial because federal agents questioned him at Guantánamo, which used sleep deprivation and other abuses to get detainees to talk.
But the potential testimony of Mr. Hamdan has already been damaging to the defense. Capt. Brian L. Mizer, Mr. Nashiri’s longest-serving lawyer, left the case this month over an ethical conflict. Captain Mizer had defended Mr. Hamdan at trial and knows something about his interrogations, which could be helpful to Mr. Nashiri. But Captain Mizer cannot divulge what he knows because of attorney-client confidentiality.
In 2011, weeks after Mr. Nashiri’s first appearance in court, Brig. Gen. Mark S. Martins, the chief prosecutor at the time, described the war court’s reliance on hearsay testimony as a necessity for a nation at war.
Hearsay testimony provides “sufficient flexibility to submit the best available evidence from genuine zones of conflict,” General Martins said in a speech to the American Bar Association.
Hearsay would be used at military commissions, he said, under “tailored exceptions that make sense given the unique circumstance of military and intelligence operations during hostilities — and the adverse impacts on such operations that would likely result from the production of the witnesses.”
He made no mention of the prosecution’s intent to use more than 100 hearsay statements that federal agents collected in the previous decade from Yemeni eyewitnesses under the supervision of Yemeni intelligence.
Jodie Blackstock, a London-based criminal defense lawyer, said hearsay should only be used “in exceptional circumstances.”
“It appears that in this case a substantial amount of the evidence against the accused is hearsay, and if that is permitted it will cast doubt on whether the trial can be fair,” said Ms. Blackstock, who observed this week’s proceedings on behalf of a British human rights organization.
