Doing so would infuriate career national security professionals and disrupt a carefully-honed approach to handling terrorism suspects, said Joshua A. Geltzer, a former Justice Department attorney. That includes the F.B.I.’s policy of delaying terror suspects’ Miranda warning rights to remain silent and have a defense lawyer during initial interrogations, he said.
“The F.B.I. would lose its mind” if Mr. Trump transferred Mr. Saipov to military custody, said Mr. Geltzer, who served as senior director for counterterrorism at the National Security Council during the Obama administration. Invoking Jim Mattis, the secretary of defense, Mr. Geltzer added: “Why would Mattis want this headache?”
Even if Mr. Saipov is not sent to Guantánamo, Mr. Trump could place him in military custody on domestic soil for prolonged interrogation without charges or access to a defense attorney, like the two suspects President George W. Bush held as “enemy combatants” in a South Carolina brig.
At a press briefing on Wednesday, Sarah Huckabee Sanders, the White House press secretary, said, “I believe we would consider this person to be an enemy combatant,” but said no decision had yet been made about how to handle him.
But by Wednesday evening, after Mr. Saipov was charged in federal court in Manhattan, it appeared the Trump administration would not declare him an enemy combatant, said Senator Lindsey Graham, Republican of South Carolina. Earlier in the day, Mr. Graham had told a news conference that Mr. Saipov should be held and interrogated as a military detainee for at least 30 days, rather than being read the Miranda warning and given a defense lawyer.
“The Trump administration missed an important opportunity to send a strong message to terrorists and make America safer,” Mr. Graham said in an evening Twitter post. “This is a huge mistake. Very sad.”
In the criminal complaint charging Mr. Saipov, the F.B.I. said it had read him the Miranda warning, but he had voluntarily waived those rights and told interrogators that he had been inspired to carry out the attack after watching Islamic State propaganda videos. It did not say whether or how long investigators had questioned him before reading the warning.
While Mr. Graham was focused on interrogation, Mr. Trump seemed to be more interested in punishment. On Wednesday, he called the civilian criminal justice system “a joke” and “a laughingstock” when it came to prosecuting terrorism cases.
“We also have to come up with punishment that’s far quicker and far greater than the punishment these animals are getting right now,” the president said. “They’ll go through court for years. And at the end, they’ll be — who knows what happens. We need quick justice and we need strong justice — much quicker and much stronger than we have right now.”
Since the Sept. 11, 2001, attacks, the Justice Department has successfully prosecuted hundreds of terrorism-related cases in civilian court. Last month, for example, it convicted Ahmad Khan Rahami, who was arrested in September 2016 for setting off bombs in New York City and now faces a life sentence. (Mr. Graham had called on the Obama administration to transfer Mr. Rahami to military custody, too.)
By contrast, the military commissions system at Guantánamo has repeatedly plunged into chaos. It has struggled to bring contested cases to trial, and several of its few convictions were overturned on appeal.
On Wednesday, for example, a judge at Guantánamo, Air Force Col. Vance Spath, held in contempt the chief defense counsel in the commissions system, Brig. Gen. John Baker. General Baker was fined $1,000 and sentenced to 21 days confinement.
The dispute centered on General Baker’s refusal to rescind his dismissal of three civilian defense lawyers from the death penalty case against a Saudi detainee, Abd al-Rahim al-Nashiri, who is accused of orchestrating the 2000 bombing of the American destroyer Cole. The lawyers had asked to quit for ethical reasons, in connection with alleged violations of attorney-client confidentiality in a matter where details remain classified.
Mr. Nashiri was charged in 2011, but his case remains mired in pretrial hearings. The departure of most of his defense team, which Colonel Spath rejected, has threatened to derail the case, underscoring the military trial system’s struggle to function.
Several legal complexities would be raised by a decision to transfer Mr. Saipov to military custody. First, while the Supreme Court in 2004 upheld the wartime detention of an American arrested in Afghanistan to prevent his return to the battlefield, it also said “indefinite detention for the purpose of interrogation is not authorized.” The court also has not addressed whether holding people arrested inside the United States is similarly lawful.
In addition, the United States is not legally at war with every radical Islamist in the world. Rather, it is at war with groups covered by Congress’s 2001 Authorization for Use of Military Force against the perpetrators of the 9/11 attacks.
Despite his apparent enthusiasm for the Islamic State, there is no public evidence Mr. Saipov — who has been in the United States since 2010 — was part of that extremist organization. Whether the 2001 law legitimately covers the Islamic State, as the government claims, is the subject of a dispute that no court has addressed.