The State Department abruptly canceled travel for thousands of refugees who had already been approved to fly to the United States, days before a deadline set by President Trump to end a resettlement program that provides safe haven for people fleeing persecution.

The cancellation of flights comes after an executive order by Mr. Trump signed on Monday, which indefinitely paused relocation to shelters. The order effectively halts the process of bringing refugees into the country, which involves multiple federal agencies as well as nonprofit organizations that welcome newcomers.

More than 10,000 refugees are currently being prepared to travel to the United States, according to government figures. Among them are Afghans who faced danger because of their ties to the United States before the military withdrawal from Afghanistan. Other refugees granted travel included people from Africa, Latin America and the Middle East.

The sudden suspension of flights was a painful blow to refugees who were following a complicated and lengthy process to enter the country legally, resettlement group officials said.

Angela Plummer, executive director of Community Refugee & Immigration Services, which resettles refugees in Columbus, Ohio, said the organization had expected dozens of arrivals on the flights that were suspended.

“These are people who followed all the rules and are now at risk,” Ms Plummer said. “It’s heartbreaking.”

The decision to pause the refugee program is in line with Mr. Trump’s promise to crack down on immigration broadly.

Under the decades-old refugee program, people who have fled their homelands due to persecution, war or other life-threatening causes can legally immigrate to the United States. Mr. Trump said continuing to receive them would burden communities that were not equipped to handle them, according to the order he signed Monday.

The State Department accompanied his order with a memorandum on Tuesday that said “all previously planned refugee travel to the United States is being canceled and no new travel reservations will be made.” Organizations such as the International Rescue Committee and others helping refugees, it said, “should not request travel for any additional refugee cases at this time.”

On Wednesday, US refugee officials at homeland security agencies such as US Citizenship and Immigration Services were told to stop making decisions on refugee cases, according to an internal memo obtained by The New York Times.

News that the Trump administration has canceled travel even for refugees who have already been cleared to resettle in communities across the United States shocked leaders of nonprofits contracted by the State Department to help newcomers.

“This abrupt end to refugee admissions is devastating for families who have already suffered unimaginable persecution and waited years for a chance to rebuild their lives in safety,” Krish O’Mara Vignarajah, head of Global Refuge, said in a statement.

“Refugees go through one of the most rigorous vetting processes in the world,” she continued, “and it’s heartbreaking to see their dreams of safety derailed just days before, or in some cases, just hours before they were supposed to start their new life here.”

Eskinder Negash, president of the US Committee on Refugees and Immigrants, said that “many people have waited years, and in some cases decades, in refugee camps and have diligently gone through the refugee process to be approved to travel.”

“Even if the refugee program is reopened in the future, the indefinite suspension of refugee travel and processing will traumatize and affect refugees and families,” he said.

Ms Plummer said her group had received calls from distraught clients who had waited years for relatives to arrive, only to realize the prospect of reunification was now bleak.

Among them is Nur Ahmed, who arrived in Columbus in 2010 after fleeing the civil war in Somalia. He sponsored his child, young sister and mother to join him.

Their case was stalled during Mr. Trump’s first term as president.

Mr. Ahmed’s son and sister, both in their 20s, arrived last week, just before he returned to the White House. But his mother (70) is expected at the beginning of next month, and her arrival could be postponed indefinitely.

“I am very happy that my son and sister arrived, but I am sad that my mom was left behind,” he said.

Members of the same family are often assigned different travel dates, and in this case it can mean several years apart.

“Trump used to delay us; now he’s back and he’s late again,” said Mr. Ahmed, who is a truck driver. “All I feel is pain since Donald Trump has arrived again.”

“I haven’t seen my mom since I left and I don’t know when I’ll see her again,” he said in an interview while transporting dry food on a highway in Texas.

As part of an avalanche of executive orders to cut immigration, Mr. Trump suspended the refugee resettlement program effective Jan. 27. Resettlement agency officials had hoped that refugees who had completed the years-long process and had booked flights would still be able to travel to the United States.

In his first administration, Mr. Trump dismantled the refugee program by imposing additional levels of vetting on applicants he deemed a security risk and lowering the target for the number the United States was willing to accept.

The president makes an annual decision on how many refugees the United States is willing to accept in a given year, and the numbers have varied, with Republican presidents historically setting some of the highest limits.

However, the number of refugees admitted to the country fell to the lowest number on record, to around 11,000 in 2020, the last year of Mr. Trump in office, down from 85,000 in 2016 under President Barack Obama. He gave priority to religious minorities, mostly white Christians from countries like Moldova and Russia.

President Biden has rebuilt the program, and refugee admissions have soared, reaching 100,000 last year, the most in three decades.

This time, Mr. Trump has justified the suspension of refugee admissions on the grounds that they strain the resources of cities meant to benefit Americans.

“The United States lacks the ability to absorb large numbers of migrants, especially refugees, into its communities in a way that does not jeopardize the availability of resources for Americans,” the order, signed by Mr. Trump within hours of his inauguration.