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.