The first former Guantánamo detainee to be tried in a civilian court was acquitted on Wednesday of all but one of more than 280 charges of conspiracy and murder in the 1998 terrorist bombings of the United States Embassies in Nairobi, Kenya, and Dar es Salaam, Tanzania.
The case has been seen as a test of President Obama’s goal of trying detainees in federal court whenever feasible, and the result seems certain to fuel debate over whether civilian courts are appropriate for trying terrorists.
Because of the unusual circumstances of Mr. Ghailani’s case — after he was captured in Pakistan in 2004, he was held for nearly five years in a so-called black site run by the Central Intelligence Agency and at Guantánamo Bay, Cuba — the prosecution faced significant legal hurdles even getting his case to trial.
On the eve of Mr. Ghailani’s trial last month, the government lost a key ruling that may have seriously damaged its chances of winning convictions.
In the ruling, the judge, Lewis A. Kaplan of Federal District Court in Manhattan, barred prosecutors from using an important witness against Mr. Ghailani because the government had learned about the man through Mr. Ghailani’s interrogation while he was in C.I.A. custody, where his lawyers say he was tortured.
The witness, Hussein Abebe, would have testified that he had sold Mr. Ghailani the TNT used to blow up the embassy in Dar es Salaam, prosecutors told the judge, calling him “a giant witness for the government.”
The judge himself recognized the significance of excluding the witness when he said in his ruling that Mr. Ghailani’s status of “enemy combatant” probably would permit his detention as something akin “to a prisoner of war until hostilities between the United States and Al Qaeda and the Taliban end, even if he were found not guilty.”
Mr. Ghailani, who remains in custody, faces 20 years to life in prison when he is sentenced on Jan. 25.
The unexpected verdict by the anonymous six-man, six-woman jury came on the fifth day of deliberations. On Monday, the prospect of a deadlock was raised when a juror asked to be removed because she was alone in her view of the case and felt she was being attacked by other jurors. After the verdict on Wednesday, the jurors were to be taken from the courthouse by federal marshals and were unavailable for comment.
Mr. Ghailani’s lawyers, including Peter E. Quijano, Steve Zissou, Michael K. Bachrach and Anna N. Sideris, had argued that their client was innocent and had been duped into assisting in the terrorist conspiracy.
“This verdict is a reaffirmation that this nation’s judicial system is the greatest ever devised,” Mr. Quijano said outside the courthouse. “It is truly a system of laws and not men, where, in the shadow of the World Trade Center, this jury acquitted Ahmed Khalfan Ghailani of 284 out of 285 counts.”
Throughout the case, Mr. Ghailani seemed at ease with his lawyers, smiling frequently. After the verdict was read, he hugged them warmly.
The verdict came after a four-week trial in which prosecutors built a circumstantial case to try to establish that Mr. Ghailani had played a key logistical role preparing for the Tanzania attack.
They said the evidence showed that he helped to buy the Nissan Atlas truck that was used to carry the bomb, and gas tanks that were placed inside the truck to intensify the blast. He also stored an explosive detonator in an armoire he used, and his cellphone became the “operational phone” for the plotters before the attacks, prosecutors contended.
The attacks, orchestrated by Al Qaeda, killed 224 people, including 12 Americans, and injured thousands of others.
The Ghailani trial was the second stemming from the 1998 embassy attacks. In 2001, four Qaeda operatives were convicted of participating in the same conspiracy; in that trial, prosecutors were able to use three of the defendants’ statements, made to the F.B.I., in which they incriminated themselves in the plot.
In Mr. Ghailani’s trial, prosecutors chose not to introduce any of the statements Mr. Ghailani made when he was interrogated while in C.I.A. custody and at Guantánamo, although prosecutors told the judge the statements amounted “to a confession” of his role in the embassy plot. Defense lawyers argued that the statements had been coerced and were inadmissible.
Preet Bharara, the United States attorney for the Southern District of New York, said that his office would seek a life sentence for Mr. Ghailani.
Mr. Bharara expressed his “deep appreciation for the unflagging commitment, dedication and talent of the agents who so thoroughly investigated this case and the prosecutors who so ably tried it.”
As the proceeding ended, the prosecutors, including Michael Farbiarz, Harry Chernoff, Nicholas Lewin and Sean S. Buckley, approached Mr. Ghailani’s lawyers, shaking hands and exchanging quiet words.
Although the government’s loss on significant counts will undoubtedly test the Obama administration’s resolve on using civilian courts, Judge Kaplan issued two major pretrial rulings that allowed Mr. Ghailani’s prosecution to go forward and could ease the way for future detainees, like Khalid Shaikh Mohammed, the professed 9/11 mastermind, to be tried in federal court.
In May, the judge rejected a motion by Mr. Ghailani’s lawyers seeking dismissal of charges on grounds that his torture while in C.I.A. custody was outrageous government misconduct. And in the summer, the judge ruled that Mr. Ghailani’s years of detention before being brought into the civilian system had not violated his constitutional right to a speedy trial.
Mr. Mohammed has been detained since 2003, and accusations of torture, including waterboarding, would most certainly be raised in his case.
The verdict drew strong reaction from family members who had attended the trial. Susan F. Hirsch, whose husband, Abdurahman Abdalla, was killed in the Tanzania attack, said she was grateful for the jury’s efforts, but added, “I can’t help but feel that the evidence in the case would have been stronger had Ghailani been brought to trial when he was captured in 2004.”
Sue Bartley, who lost two family members in the Nairobi embassy attack — her husband, Julian L. Bartley Sr., the consul general; and her son, Julian L. Bartley Jr., a college student who was an intern — said she was “disappointed in the jury.”
“I think our prosecuting attorneys had the evidence,” she said. “I’m not sure that this jury understood what was in front of them.”
Judge Kaplan told the jurors they had demonstrated that “American justice can be rendered calmly, deliberately and fairly by ordinary people, people who are not beholden to any government, not even ours.”
“It can be rendered with fidelity to the Constitution,” he added. “You have a right to be proud of your service in this case.”