Marlon Luna said he and his girlfriend came into the United States three months ago after fleeing death threats in Venezuela. They waited in Mexico for four long months to secure a Border Patrol appointment instead of crossing illegally. Then they wound up in a New York migrant shelter.

Now, they fear that New York — and America — may be over for them.

On Thursday, the Trump administration issued a memo that widened the scope of people it would seek to deport, including those who, like Mr. Luna, used CBP One, a mobile app, to enter the country.

The Biden administration had used the app to manage the movement of 900,000 migrants through legal ports of entry. Mr. Luna, 23, said he had assumed that if he followed the rules he would have a fair shake. Now, he fears, deportation could happen at any time.

“Some people crossed illegally, but some people wanted to enter in the way that one should,” he said in Spanish outside a Randall’s Island shelter on Friday. “What we are hearing here, and really what everyone is saying, is that at any moment something could happen.”

For nearly three years, thousands of migrants have come to New York City under Biden-era programs that allowed migrants from Venezuela, Haiti and elsewhere to legally enter the United States and temporarily remain for as long as two years. Now the Homeland Security Department has empowered Immigration and Customs Enforcement officials to expel those with a temporary legal status known as parole, which also allows migrants to work here.

The new directive could have an outsize impact in New York City, where more than 225,000 migrants have arrived since early 2022, many under parole. It raised the possibility that the city’s 187 migrant shelters, where more than 49,000 people still reside, would be prime targets if ICE aggressively pursues migrants allowed in under the Biden administration.

The action in Washington came as officials in New York City, a liberal stronghold with an additional 400,000-some immigrants with temporary or no legal status, have been bracing for an immigration crackdown.

The city has so-called sanctuary laws, which limit cooperation with federal immigration authorities. City agencies have been racing to issue guidance to schools, shelters and social services offices on how to respond if ICE officers show up.

In a message to agency heads last month, Camille Joseph Varlack, who is chief of staff to Mayor Eric Adams, said that leaders would “stand firmly by the values that have made New York City a thriving city of immigrants, regardless of immigration status.”

However, Mr. Adams’s public messaging and remarks have done little to reassure people who work with immigrants and his fellow Democrats, instead creating a sense of dissonance and discombobulation.

Mr. Adams has denigrated aspects of the sanctuary laws and expressed support for modifying them to allow the city to work with ICE to deport people charged with crimes — all while declining to publicly criticize Mr. Trump. The mayor faces a trial on federal corruption charges in April and has moved to stay in the good graces of Mr. Trump, who could pardon him.

On Thursday evening, when Mr. Adams was asked about a newly issued Justice Department memo that threatens prosecution for local officials who fail to comply with the president’s immigration initiatives, the mayor signaled that he was inclined to cooperate.

“If the federal government is stating that you cannot interfere with the actions, we can’t do anything that is going to jeopardize city employees,” Mr. Adams said, adding, “We need to read through these executive orders and fully understand what they’re saying, what our authorizations may be and what they are not.”

A spokeswoman for Mr. Adams said in a statement Friday that the mayor believes that “federal immigration enforcement should be focused on the small number of people who are entering our localities and committing violent crimes.”

She added, “While the mayor and president will not always agree on everything, Mayor Adams is focused on how we can work together to do what is best for New York City.”

The measured tone from City Hall was in contrast with that of the New York attorney general, Letitia James, a Democrat. She, along with 10 other attorneys general, responded to the Justice Department memo with a fiery statement: “These vague threats are just that: empty words on paper,” the statement said. “But rest assured, our states will not hesitate to respond if these words become illegal actions.”

Under current city guidelines, federal immigration authorities can only be allowed into a shelter if they have judicial warrants for specific people. Some immigration lawyers said that they had not heard of ICE showing up at New York City shelters since the migrant crisis began almost three years ago.

But they speculated whether that would change soon if Mr. Trump decides to go after migrants who entered using CBP One or under the program that allows certain migrants from Cuba, Nicaragua, Venezuela and Haiti to legally stay for as long as two years. Mr. Trump and his allies have long criticized the programs as tactics abused by the Biden administration to allow illegal immigration under the guise of legal migration, and have moved quickly to end them.

“They’re intending to cast as wide a net as possible to really try to remove as many people who were admitted in the last two years,” said Jodi Ziesemer, the co-director of the Immigrant Protection Unit at the New York Legal Assistance Group. “We’re talking about tens of thousands of people, mostly families, who could be rounded up and deported. They’re very vulnerable.”

Accomplishing the directives in the Homeland Security memo would be a significant escalation of arrests and deportations, and would present a daunting logistical challenge. Some of the immigrants might have other legal shields, such as asylum or Temporary Protected Status, lawyers said. It might also prove hard for the United States to deport people to Venezuela, given the severely strained diplomatic relations between the countries.

Migrants in city shelters, many of whom speak scant English, were left to parse Mr. Trump’s flurry of executive orders and directives this week. Many wondered whether the asylum claims they have filed in immigration court would offer them a level of protection. Rumors of ICE officers showing up at shelters have swirled in conversations and text messages. Some migrants said they were limiting their time outside the shelters, while others were urgently trying to leave the system altogether, fearful that they could be easy targets.

Pedro Cumana, a Venezuelan living in a small tent outside the Randall’s Island shelter, said in an interview in Spanish that when helicopters have flown over or sirens have gone off at night this week, he has poked his head outside, wondering whether it’s immigration officials or a routine police run.

“I haven’t been able to sleep well,” said Mr. Cumana, who has a hearing related to his asylum claim this month. “I feel uncertain. I’m not sure how to feel, because what if at my own court hearing they arrest me? It’s not easy. You don’t know what to expect.”

Immigration lawyers and activists expressed outrage at the memo’s suggestion that immigration officials could retroactively strip migrants of parole status and seek to move them from formal deportation proceedings to a sped-up exit.

“The barrage of things that have happened this past week is very intentional, obviously,” said Deborah Lee, the lawyer in charge of the immigration law unit at The Legal Aid Society. “But it’s also intended to be so overwhelming that people cannot fight back and make legal challenges because of the full volume of everything.”

Still, other migrants, like Ramon Cortez, 43, also from Venezuela, refused to panic about what was brewing in the news and on social media. Mr. Cortez, who arrived in New York two months ago after using the CBP One app to enter the country, said in an interview in Spanish that he would not fret until he received official notice that he was at risk of deportation.

“If I receive a formal document, a court or something that tells me, ‘This is going to happen there,’ I’m going to start to believe what they’re saying,” he said.

Wesley Parnell, Olivia Bensimon and Dana Rubinstein contributed reporting.