The Trump administration has sent hundreds of Venezuelans accused of being gang members to a prison in El Salvador, pushing the limits of U.S. immigration law by carrying out the deportations seemingly after a federal judge ordered that the flights not proceed.

While the precise timing of the deportations remained unclear, White House officials exulted that they had carried out the transfer to a notorious Central American prison. U.S. courts, however, have just begun to wrestle with the serious legal questions raised by a new executive order that Trump officials hope will help them carry out many more rapid-fire expulsions.

President Nayib Bukele of El Salvador posted a three-minute video on social media on Sunday of men in handcuffs being led off a plane during the night and marched into prison. The video also shows prison officials shaving the prisoners’ heads.

The Trump administration hopes that the unusual prisoner transfer deal — not a swap but an agreement for El Salvador to take suspected gang members — will be the beginning of a larger effort to use the Alien Enemies Act of 1798 to rapidly arrest and deport those it identifies as members of Tren de Aragua without many of the legal processes common in immigration cases.

The Alien Enemies Act allows for summary deportations of people from countries at war with the United States. The law, best known for its role in the internment of Japanese Americans during World War II, has been invoked three times in U.S. history — during the War of 1812, World War I and World War II — according to the Brennan Center for Justice, a law and policy organization. American officials familiar with the deal said that the United States would pay El Salvador about $6 million to house the prisoners.

On Saturday, Judge James E. Boasberg of Federal District Court in Washington issued a temporary restraining order blocking the government from deporting any immigrants under the law after President Trump issued an executive order invoking it.

In a hastily scheduled hearing sought by the American Civil Liberties Union, the judge said he did not believe federal law allowed the president’s action, and ordered that any flights that had departed with Venezuelan immigrants under Trump’s executive order return to the United States “however that’s accomplished — whether turning around the plane or not.”

“This is something you need to make sure is complied with immediately,” he said.

A lawyer representing the government, Drew Ensign, told the judge that he did not have many details to share, and that describing operational details would raise “national security issues.”

The precise timing of the flights to El Salvador is important because Judge Boasberg issued his order shortly before 7 p.m. in Washington, but video posted from El Salvador shows the deportees disembarking the plane at night. El Salvador is two time zones behind Washington, which raises questions about whether the Trump administration ignored an explicit court order.

Judge Boasberg’s order to turn flights around came after he told the government earlier on Saturday not to deport five Venezuelan men who were the initial focus of the legal fight. The Trump administration is appealing Judge Boasberg’s order.

On Sunday, Mr. Bukele posted a screenshot on social media about Judge Boasberg’s order and wrote, “Oopsie… Too late.” Secretary of State Marco Rubio later shared Mr. Bukele’s post from his personal account.

Attorney General Pam Bondi criticized the judge on Saturday night in a written statement that said that he had sided with “terrorists over the safety of Americans,” and that his order “disregards well-established authority regarding President Trump’s power, and it puts the public and law enforcement at risk.”

On Sunday, the government of Venezuela denounced the transfer, saying that it flew in the face of U.S. and international laws, adding that the attempt to apply the Alien Enemies Act “constitutes a crime against humanity.”

The statement compared the transfer to “the darkest episodes of human history,” including slavery and Nazi concentration camps. In particular, the government denounced what it called a threat to kidnap minors as young as 14 by labeling them as terrorists, claiming that the minors were “considered criminals simply for being Venezuelan.”

The government of President Nicolás Maduro of Venezuela has presented an obstacle to the Trump administration as it plans to step up deportations — and to target suspected Tren de Aragua members — because for years it has not regularly accepted deportation flights. In recent weeks, Mr. Maduro has gone back and forth on whether his government will accept flights of Venezuelans deported by the United States.

As a result, the Trump administration has sought alternative destinations for Venezuelans, including the naval base at Guantánamo Bay, Cuba, where it has sent migrants including accused gang members, though it has since removed them from the base.

In an unusual turn, El Salvador has presented Mr. Trump with another alternative.

In early February, while Secretary of State Marco Rubio was visiting El Salvador, Mr. Bukele offered to take in deportees of any nationality, including convicted criminals, and jail them in part of El Salvador’s prison system, for a fee.

Mr. Rubio, who announced Mr. Bukele’s offer at the time, said that the Salvadoran president had agreed to jail “any illegal alien in the United States who is a criminal of any nationality, whether from MS-13 or the Tren de Aragua.”

Officials from both the United States and El Salvador revealed that the deal with the Trump administration also included the transfer of suspected members of the Salvadoran gang MS-13 who were being held in the United States awaiting charges.

“We have sent 2 dangerous top MS-13 leaders plus 21 of its most wanted back to face justice in El Salvador,” Mr. Rubio posted on social media on Sunday. Mr. Rubio added that “over 250 alien enemy members of Tren de Aragua” had also been sent to El Salvador, which “has agreed to hold in their very good jails at a fair price.”

The two MS-13 men mentioned by Mr. Rubio were an accused top leader indicted in 2020 on Long Island on federal charges including terrorism and an accused gang member charged in Newark in February with entering the United States illegally.

The first, Cesar Humberto Lopez-Larios, was among 14 of the gang’s highest-ranking leaders who were charged on Long Island in 2020. He was arrested last year in Texas and has since been in U.S. custody awaiting trial.

The second, Cesar Eliseo Sorto-Amaya, was arrested in February on charges that he entered the United States illegally — for the fourth time since 2015. He was wanted on double aggravated homicide charges in El Salvador, where he had been sentenced in absentia to 50 years in prison. The U.S. charges against both men were dismissed on Wednesday, according to court records that were unsealed on Sunday.

The prosecutors in Mr. Lopez-Larios’s case offered the following reasoning in a letter to the judge for seeking the dismissal of the charges against him. “The United States has determined that sensitive and important foreign policy considerations outweigh the government’s interest in pursuing the prosecution of the defendant,” the letter said.

The two men’s transfers have raised concerns among some U.S. law enforcement officials, who fear that those individuals, once out of U.S. custody, could escape or issue orders that may endanger witnesses in both countries, according to people familiar with the matter who spoke on the condition of anonymity to describe internal discussions.

Mr. Bukele came to power on promises to crack down on gang violence and MS-13. His success in restoring safety has won him broad support in El Salvador and around Latin America, but critics say that it has come at the cost of human rights.

By imposing a state of emergency, the Salvadoran leader has sidestepped due process and ordered sweeping arrests that have ensnared thousands of people without any affiliation to criminal groups, critics say. Under Mr. Bukele, the prison population has soared and abuses, including torture, have been documented in the system.

Mr. Bukele has promoted his iron-fisted approach by posting dramatic photographs from his country’s prisons that resemble those shared this weekend: They often feature scores of tattooed inmates with shaved heads held in handcuffs and forced into submissive poses.

Tim Balk contributed reporting.