By Ben ConeryThe Obama administration’s plan to prosecute suspected terrorists in civilian courts was dealt a serious blow Wednesday when a jury acquitted a former Guantanamo detainee of all but one of the hundreds of charges he faced.

Ahmed Ghailani, 36, still faces at least 20 years in prison and could receive a life sentence after he was convicted of one count of conspiracy to destroy U.S. property in connection with the 1998 bombings of U.S. embassies in Kenya and Tanzania.

But Ghailani was acquitted of 224 counts of murder for each of the people killed in the bombings as well as other 60 other charges. He could have faced the death penalty if convicted of murder.

The trial at a Lower Manhattan courthouse had been viewed as a test for the Obama administration’s aim of putting other terrorist suspects, including self-professed Sept. 11 mastermind Khalid Shaikh Mohammed and four others held at Guantanamo Bay, Cuba, on trial on U.S. soil.

The verdict also gave fuel to persistent administration critics who argue that suspected terrorists should be prosecuted by military tribunals at Guantanamo not in U.S. civilian courts.

Rep. Peter T. King, a New York Republican who is the ranking member of the Committee on Homeland Security, called on the administration to abandon plans to prosecute terrorists in civilian courts, saying the “tragic verdict demonstrates the absolute insanity of the Obama administration’s decision to try al Qaeda terrorists in civilian courts.”

“I am disgusted at the total miscarriage of justice today in Manhattan’s federal civilian court,” Mr. King said in a statement. “In a case where Ahmed Khalfan Ghailani was facing 285 criminal counts, including hundreds of murder charges, and where Attorney General Eric Holder assured us that ‘failure is not an option,’ the jury found him guilty on only one count and acquitted him of all other counts including every murder charge.”

The Obama administration didn’t address such criticisms Wednesday and focused instead on the one charge on which Ghailani was convicted.

“We respect the jury’s verdict and are pleased that Ahmed Ghailani now faces a minimum of 20 years in prison and a potential life sentence for his role in the embassy bombings,” Justice Department spokesman Matthew Miller said in a statement.

Ghailani’s prosecution demonstrated some of the constitutional challenges the government would face if that happens. On the eve of his trial last month, the judge barred the government from calling a key witness because the witness had been identified while Ghailani was being held at a secret CIA prison where harsh interrogation techniques were used.

After briefly considering an appeal of that ruling, prosecutors forged ahead with a case honed a decade ago in the prosecution of four other men charged in the same attacks in Tanzania and Kenya. All were convicted in the same courthouse and sentenced to life terms.

Prosecutors said Ghailani helped an al Qaeda cell buy a truck and components for explosives used in a suicide bombing in his native Tanzania on Aug. 7, 1998. The attack in Dar es Salaam and a nearly simultaneous bombing in Nairobi, Kenya, killed 12 Americans.

The day before the bombings, Ghailani boarded a one-way flight to Pakistan under an alias, prosecutors said. While on the run, he spent time in Afghanistan as a cook and bodyguard for Osama bin Laden and later as a document forger for al Qaeda, authorities said.

He was captured in 2004 in Pakistan and was held by the CIA at a secret overseas camp. In 2006, he was transferred to Guantanamo and held until the decision last year to bring him to New York.

Despite losing its key witness, the government was given broad latitude to reference al Qaeda and bin Laden. It did again and again.

“This is Ahmed Ghailani. This is al Qaeda. This is a terrorist. This is a killer,” Assistant U.S. Attorney Harry Chernoff said in closing arguments.

The jury heard a former al Qaeda member who has cooperated with the government describe how bin Laden took the group in a more radical direction with a 1998 fatwa, or religious edict, against Americans.

Bin Laden accused the United States of killing innocent women and children in the Middle East and decided “we should do the same,” L’Houssaine Kherchtou said on the witness stand.

A prosecutor read aloud the fatwa, which called on Muslims to rise up and “kill the Americans and plunder their money wherever and whenever they can find it.”

Other witnesses described how Ghailani bought gas tanks used in the truck bomb with cash supplied by the terror group, how the FBI found a blasting cap stashed in his room at a cell hide-out and how he lied to family members about his escape, telling them he was going to Yemen to start a new life.

The defense never contested that Ghailani knew some of the plotters. But it claimed he was in the dark about their sinister intentions.

“Call him a fall guy. Call him a pawn,” Mr. Quijano said in his closing argument. “But don’t call him guilty.”

Mr. Quijano argued the investigation in Africa was too chaotic to produce reliable evidence. He said local authorities and the FBI “trampled all over” unsecured crime scenes during searches in Tanzania.

The verdict came after the anonymous jurors deliberated over seven days. Ghailani rubbed his face, smiled and hugged his lawyers after the jurors filed out of the courtroom.

U.S. District Judge Lewis Kaplan had thanked the jury, saying the outcome showed that justice “can be rendered calmly, deliberately and fairly by ordinary people, people who are not beholden to any government, even this one.”

Ghailani will be sentenced Jan. 25.

Defense attorney Peter Quijano welcomed the acquittals. He said the one conviction would be appealed.

“We still truly believe he is innocent of all these charges,” Mr. Quijano said. Still, Ghailani, who could have faced a mandatory life sentence if convicted of some of the other counts, “believed he got a fair trial,” he added.

Prosecutors had branded Ghailani a cold-blooded terrorist. The defense portrayed him as a clueless errand boy, exploited by senior al Qaeda operatives and framed by evidence from contaminated crime scenes.

c This article is based in part on wire service reports.