A federal judge gave the Trump administration until the end of Monday to return to the United States a Maryland man who was inadvertently deported to El Salvador last month despite a court order allowing him stay in the country.

In a brief ruling issued on Friday, the judge, Paula Xinis, said that federal officials had acted without “legal basis” last month when they arrested the man, Kilmar Armando Abrego Garcia, and put him on a plane — with no due process — to a notorious Salvadoran megaprison.

The decision by Judge Xinis, which came during a hearing in Federal District Court, was a sharp rebuke to the Trump administration. In court papers filed this week, administration officials had said there was little they could do to get Mr. Abrego Garcia back from El Salvador, even after acknowledging that his deportation on March 15 had been a mistake.

The judge’s ruling could put her on a collision course with the White House. President Trump and some of his top aides have repeatedly and aggressively attacked other federal judges who have questioned their attempts to carry out their deportation policies.

Hours after the hearing on Friday, the Justice Department said that it intended to appeal the decision.

The case of Mr. Abrego Garcia, a Salvadoran migrant whose wife and three children are U.S. citizens, has become the latest flashpoint in a multifront battle between immigration lawyers and the White House, which has been ramping up deportations using both traditional and unusual methods.

The case has also highlighted the Trump administration’s efforts to accuse migrants of being members of violent street gangs as a way to accelerate their removal from the country.

In court filings, the Justice Department has accused Mr. Abrego Garcia, 29, of belonging to a transnational gang with roots in El Salvador called MS-13. But officials have offered only limited evidence to support their claims, and Mr. Abrego Garcia has denied them.

During the hearing on Friday, Judge Xinis expressed skepticism about any ties Mr. Abrego Garcia has to MS-13, noting there was little proof that he belonged to the gang.

“In a court of law, when someone is accused of membership in such a violent and predatory organization, it comes in the form of an indictment, complaint, criminal proceeding — a robust process, so we can address the facts,” Judge Xinis said. “I haven’t yet heard that from the government.”

Outside the courthouse, Jennifer Stefania Vasquez Sura, Mr. Abrego Garcia’s wife, celebrated the decision with a cheering crowd of supporters.

“We will continue fighting for Kilmar, for my husband,” she said.

In the hearing, the Justice Department appeared to recognize that it had a weak hand.

Erez Reuveni, a department lawyer, admitted to the judge that Mr. Abrego Garcia should not have been deported in the first place, and told her that he had been frustrated with the case after it landed on his desk.

Mr. Reuveni sought what appeared to be a compromise, asking for 24 hours to persuade his “client” — the Trump administration — to begin the process of retrieving Mr. Abrego Garcia from the prison, which is known as the Terrorism Confinement Center.

“Good clients listen to their lawyers,” Judge Xinis told him.

But she ultimately rejected his request by imposing a deadline of 11:59 p.m. on Monday for Mr. Abrego Garcia to be brought back to the United States.

Wendy Ramos, a spokeswoman for El Salvador’s president, did not immediately respond to a request for comment on whether the government intended to turn Mr. Abrego Garcia over to U.S. authorities.

Mr. Abrego Garcia came to the United States illegally in 2011, court papers say, in order to be near his older brother in Maryland. He lived quietly, starting a family with Ms. Sura, until March 2019, when he was taken into custody by the local police while looking for casual labor outside a Home Depot.

U.S. Immigration and Customs Enforcement quickly took control of his case and began an effort to deport him, based in part on accusations that he was a member of MS-13.

But in October 2019, Mr. Abrego Garcia persuaded an immigration judge that he might face violence, even torture, if returned to his homeland. The judge granted him a special status called “withholding from removal” that permitted him to avoid being deported.

Last month, after nearly six years had passed, Mr. Abrego Garcia was stopped again by immigration agents who incorrectly told him that his protected status had changed.

He was arrested, and within three days had been placed on one of three flights to El Salvador that the Trump administration had hastily arranged using a rarely invoked 18th-century wartime statute, the Alien Enemies Act, to deport a group of Venezuelan men accused of being members of a different gang, Tren de Aragua.

Two of the planes were sent to El Salvador under the authority of the wartime act, administration officials have said. But the third flight — the one on which Mr. Abrego Garcia was traveling — was supposed to have been transporting only migrants with formal removal orders signed by a judge.

Simon Sandoval-Moshenberg, a lawyer for Mr. Abrego Garcia, told reporters after the Friday hearing that he hoped a victory in the case would set a precedent in the cases of other men deported to the Salvadoran prison, by showing that the government had the ability to return them to the United States.

Mr. Sandoval-Moshenberg added that he appreciated that Mr. Reuveni, the Justice Department lawyer, “recognized the seriousness of the case.” But he rued the fact that the Trump administration had not been cooperative so far in bringing his client back.

“This wasn’t the evil of ill intent toward Kilmar,” Mr. Sandoval-Moshenberg said. “It was the evil of apathy as to whether or not they deport the right person.”

Annie Correal contributed reporting from Mexico City.