WASHINGTON — After working for a year to redeem the international reputation of military commissions, Obama administration officials are alarmed by the first case to go to trial under revamped rules: the prosecution of a former child soldier whom an American interrogator implicitly threatened with gang rape.

The defendant, Omar Khadr, was 15 when he was captured in Afghanistan and accused of throwing a grenade that killed an American soldier. Senior officials say his trial is undermining their broader effort to showcase reforms that they say have made military commissions fair and just.

“Optically, this has been a terrible case to begin the commissions with,” said Matthew Waxman, who was the Pentagon’s top detainee affairs official during the Bush administration. “There is a great deal of international skepticism and hostility toward military commissions, and this is a very tough case with which to push back against that skepticism and hostility.”

Senior officials at the White House, the Justice Department and the Pentagon have agreed privately that it would be better to reach a plea bargain in the Khadr case so that a less problematic one would be the inaugural trial, according to interviews with more than a dozen current and former officials. But the administration has not pushed to do so because officials fear, for legal and political reasons, that it would be seen as improper interference.

Mr. Khadr’s trial at the naval base in Guantánamo Bay started earlier in August but was put on a monthlong hiatus because a lawyer got sick and collapsed in court. The pause has allowed the administration to consider the negative images the trial has already generated.

Chief among them are persistent questions about the propriety of prosecuting a child soldier. Moreover, in a blow to establishing an image of openness, the Pentagon sought to ban journalists who wrote about publicly known information that it decreed should be treated as secret.

The judge declined to suppress statements Mr. Khadr made after an Army interrogator sought to frighten him with a fabricated story about an Afghan youth who disappointed interrogators and was sent to an American prison where he died after a gang rape. In a pretrial hearing, the interrogator confirmed making that implicit threat, but the judge ruled it did not taint Mr. Khadr’s later confessions.

And prosecutors disqualified an officer from the jury because he said he agreed with President Obama that Guantánamo had compromised America’s values and international reputation.

Administration officials would speak only anonymously about deliberations on whether to try to abort the trial. But their view about the need to improve the system’s perceived credibility — so allies will cooperate by providing evidence or extraditing defendants — was echoed by Kenneth L. Wainstein, assistant attorney general for national security in the Bush administration.

“It is important for the government to be able to proceed through a trial, to do so in a transparent way, and have the world see that this is a fair process with strong safeguards and full due process,” he said. “The sooner that happens, the better.”

No one intended the Khadr case to be the first trial under the revamped system.

He had already been charged when Mr. Obama froze the tribunals in January 2009. In November, after Congress overhauled commission rules, Attorney General Eric H. Holder Jr. included Mr. Khadr in an initial batch of five detainees who would remain in the military system.

At the time, officials say, it was assumed that other referrals would quickly follow. But controversy over Mr. Holder’s decision to move five other detainees to the regular court system for a trial in New York over the Sept. 11 attacks shut down the process, and military prosecutors resumed Mr. Khadr’s case.

Mr. Khadr, who was born in Toronto and comes from a Qaeda-linked family, was a teenager in 2002 when he was found, heavily wounded, at a compound in Afghanistan after a firefight with United States troops. A grenade blast in that battle killed an Army sergeant, Christopher Speer.

Investigators concluded that Mr. Khadr threw the grenade — a theory defense lawyers reject. A videotape found at the compound was said to show Mr. Khadr helping to make and plant roadside bombs. But the centerpiece of five charges against him is Sergeant Speer’s killing.

Earlier this summer, prosecutors and retired Vice Adm. Bruce MacDonald, the commissions’ convening authority who must approve any sentence, apparently raised the possibility of a deal that would allow Mr. Khadr to serve only a few years, rather than a potential life sentence, if he pleaded guilty.

But Mr. Khadr, now 23, reacted by firing two defense lawyers. He told the court he was offended by what he saw as an attempt to “legitimize the sham process” by dangling “the least sentence possible” to coerce a confession.

Still, Dennis Edney, a Canadian lawyer assisting the Khadr family, said a deal involving a lesser charge, like conspiracy to support terrorism, remained possible.

“I would strongly recommend a reasonable deal to Omar if the murder charge was off the table,” Mr. Edney said.

Sergeant Speer’s wife, Tabitha Speer, might object to that outcome. She attended the opening of the trial and has written of her husband’s death, “The pain now carried by both myself and our children will last a lifetime.”

Administration officials have discussed whether senior civilian leaders at the Pentagon or elsewhere could get involved, helping to revive plea negotiations or even directing Admiral MacDonald to make a more attractive offer. (Admiral MacDonald did not respond to an interview request.)

A similar high-level intervention would clearly be allowed in the regular court system, where the attorney general supervises prosecutions. But tribunal rules insulate commission officials.

A provision in the Military Commissions Act prohibits “unlawful command influence,” defined as attempting “to coerce, or, by any unauthorized means, influence” the judgment or actions of prosecutors or the convening authority. Officials are debating what that means.

The provision’s wording was suggested to lawmakers in 2006 by Col. Morris D. Davis, then the chief commissions prosecutor, who complained that Bush appointees had inappropriately pressured him to take aggressive steps like using evidence he considered tainted by torture.

Now retired, Colonel Davis said he believes the provision was not meant to bar pressure to sweeten a plea offer: “It’s clearly not ‘command influence’ to do something favorable to the accused,” he said. “The whole concept was the opposite of that.”

Still, the statute makes no such distinction. And officials do not want to risk intervening, lest it become partisan ammunition for conservatives who might accuse them of using political interference to coddle a terrorist.

Eugene R. Fidell, who teaches military law at Yale Law School, said there was “ no clear answer” to how far administration officials may intrude. But given the risks, he said, “they are right to be cautious.”