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 seemingly after a federal judge ordered that the deportation flights not proceed.

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.

“Today, the first 238 members of the Venezuelan criminal organization, Tren de Aragua, arrived in our country,” Mr. Bukele wrote, adding that “The United States will pay a very low fee for them, but a high one for us.”

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.

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 to 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 them disembarking the plane at night. El Salvador is two time zones behind Washington, raising questions about whether the Trump administration ignored an explicit court order.

On Sunday, Mr. Bukele posted a screenshot on social media about Judge Boasberg’s order and wrote, “Oopsie… Too late.”

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.”

Officials from both countries 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,” Secretary of State Marco Rubio posted on social media on Sunday. Mr. Rubio added that “over 250 alien enemy members of Tren de Aragua” were also sent to El Salvador, which “has agreed to hold in their very good jails at a fair price.”

Two of those MS-13 defendants are charged as senior members of the international criminal organization.

The Trump administration has faced problems deporting Venezuelans, hundreds of thousands of whom entered the United States during a surge in migration in recent years.

Venezuela’s leader, Nicolás Maduro, is among a handful of leaders in the region whose governments have not regularly received deportation flights from the United States because of a breakdown in diplomatic relations. Since Mr. Trump took office, Mr. Maduro has gone back and forth on whether his government will receive its deported citizens.

Last month, the United States sent groups of Venezuelans to the naval base at Guantánamo Bay, Cuba, and described at least some of them as gang members. Then on Feb. 20 the Trump administration abruptly repatriated all of the Venezuelan migrants from the base in a transfer through Honduras, with one being brought back to an immigration facility in the United States.

El Salvador had also presented itself as an option for deported Venezuelans. In early February, during a visit by Mr. Rubio, Mr. Bukele offered to take in deportees of any nationality, including convicted criminals, saying he would hold them in the country’s jail system.

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.”

Tim Balk contributed reporting.