The last time Sandra Rodríguez saw her son Gerson, she bent down to look him in the eye. “Be good,” she said, instructing him to behave when he encountered Border Patrol agents on the other side of the river in the United States, and when he was reunited with his uncle in Houston.

The 10-year-old nodded, giving his mother one last squinty smile. Tears caught in his dimples, she recalled, as he climbed into a raft and pushed out across the Rio Grande toward Texas from Mexico, guided by a stranger who was also trying to reach the United States.

Ms. Rodríguez expected that Gerson would be held by the Border Patrol for a few days and then transferred to a government shelter for migrant children, from which her brother in Houston would eventually be able to claim him. But Gerson seemed to disappear on the other side of the river. For six frantic days, she heard nothing about her son — no word that he had been taken into custody, no contact with the uncle in Houston.

Finally, she received a panicked phone call from a cousin in Honduras who said that Gerson was with her. The little boy was crying and disoriented, his relatives said; he seemed confused about how he had ended up back in the dangerous place he had fled.

Hundreds of migrant children and teenagers have been swiftly deported by American authorities amid the coronavirus pandemic without the opportunity to speak to a social worker or plea for asylum from the violence in their home countries — a reversal of years of established practice for dealing with young foreigners who arrive in the United States.

The deportations represent an extraordinary shift in policy that has been unfolding in recent weeks on the southwestern border, under which safeguards that have for decades been granted to migrant children by both Democratic and Republican administrations appear to have been abandoned.

Historically, young migrants who showed up at the border without adult guardians were provided with shelter, education, medical care and a lengthy administrative process that allowed them to make a case for staying in the United States. Those who were eventually deported were sent home only after arrangements had been made to assure they had a safe place to return to.

That process appears to have been abruptly thrown out under President Trump’s latest border decrees. Some young migrants have been deported within hours of setting foot on American soil. Others have been rousted from their beds in the middle of the night in U.S. government shelters and put on planes out of the country without any notification to their families.

The Trump administration is justifying the new practices under a 1944 law that grants the president broad power to block foreigners from entering the country in order to prevent the “serious threat” of a dangerous disease. But immigration officials in recent weeks have also been abruptly expelling migrant children and teenagers who were already in the United States when the pandemic-related order came down in late March.

Since the decree was put in effect, hundreds of young migrants have been deported, including some who had asylum appeals pending in the court system.

Some of the young people have been flown back to Central America, while others have been pushed back into Mexico, where thousands of migrants are living in filthy tent camps and overrun shelters.

In March and April, the most recent period for which data was available, 915 young migrants were expelled shortly after reaching the American border, and 60 were shipped home from the interior of the country.

During the same period, at least 166 young migrants were allowed into the United States and afforded the safeguards that were once customary. But in another unusual departure, Customs and Border Protection has refused to disclose how the government was determining which legal standards to apply to which children.

“We just can’t put it out there,” said Matthew Dyman, a public affairs specialist with the agency, citing concerns that human smugglers would exploit the information to traffic more people into the country if they knew how the laws were being applied.

On Tuesday, the Trump administration extended the stepped-up border security that allows for young migrants to be expelled at the border, saying the policy would remain in place indefinitely and be reviewed every 30 days.

Chad F. Wolf, the acting secretary of the Department of Homeland Security, said the policy had been “one of the most critical tools the department has used to prevent the further spread of the virus and to protect the American people, D.H.S. front-line officers and those in their care and custody from Covid-19.”

An agency spokesman said its policies for deporting children from within the interior of the country had not changed.

Amid Mr. Trump’s efforts to block migrants from seeking refuge in the United States, the administration has been scrutinized especially for its treatment of the most vulnerable among them — children.

Beginning in 2017, the government traumatized thousands of children by separating them from their parents at the border. Administration officials have also left young migrants to languish in filthy Border Patrol holding cells with no adult supervision and argued in court that the children were not legally entitled to toothbrushes or soap.

Democratic members of Congress argue that the swift deportations taking place now violate the Trafficking Victims Protection Act, a 20-year-old federal law that lays out standards for the treatment of foreign children who arrive at the American border without an adult guardian.

In a letter last month to Mr. Wolf, Democratic members of the Senate Judiciary Committee said the moves had “no known precedent or clear legal rationale.”

Immigrant advocates say their pleas for help ensuring that the children have somewhere safe to go when they land have been ignored. Since the coronavirus was first discovered in the United States in January, 239 unaccompanied minors have been returned to Guatemala, and 183 have been returned to Honduras, according to government figures.

“The fact that nobody knows who these kids are and there are hundreds of them is really terrifying,” said Jennifer Nagda, policy director of the Young Center for Immigrant Children’s Rights. “There’s no telling if they’ve been returned to smugglers or into harm’s way.”

Some minors have been deported overnight despite an Immigration and Customs Enforcement policy that says they should be repatriated only during daylight hours.

Before daybreak one morning late last month, Pedro Buezo Romero, 16, was taken from his bed in a shelter in New York and told to pack a suitcase so he could be taken to a court appearance in Florida.

Instead, the teenager ended up on four flights over two days. He was able to sleep for a few hours in a hotel room in Miami shared by three adult employees of a private security company hired to transport him and two other migrant teenagers.

Only before boarding his final flight to Honduras from Texas did the adults reveal to Pedro that he was being deported. When he arrived in Honduras, he had to borrow the cellphone of an immigration official to ask his cousin for a place to stay.

Pedro’s mother has not been seen since the shelter in Mexico where they had been staying together was ransacked by gang members. He and his mother were separated during the ordeal, after which Pedro decided to cross the border alone.

While Pedro was in transit, his lawyers had worked frantically to try to locate him but did not receive any response from the federal government. “There were two or three days we had no idea where he was,” said Katty Vera de Fisher, a supervising migration counselor for Catholic Charities of New York.

Some of the children who have been expelled from the United States were previously ordered deported. But historically, even children with prior deportation orders have been given new opportunities to request asylum if they entered the United States again. Now, that appears to have changed.

Lawyers representing children threatened with deportation say they are having to engage in 11th-hour legal maneuvers to try to prevent deportations from happening.

Last week, Hannah Flamm, an immigration lawyer in New York, had only hours to try to stop the repatriation of a 14-year-old client after learning the girl had been booked by ICE on a 3 a.m. flight to Honduras.

The girl’s family had not been notified of her imminent arrival. Ms. Flamm managed to secure an emergency stay of the deportation at 11:47 p.m., at which point the girl was allowed to go back to sleep in the shelter where she was staying.

Ricardo Rodríguez Galo, the uncle of the 10-year-old boy who was deported this month, said he was shocked to learn that Gerson had been sent back to Honduras alone.

Mr. Rodríguez said he worried about the boy’s safety in Honduras, where his sister’s former partner had beaten the boy and his mother and withheld food from them. Mr. Rodríguez also wondered about the judgment of American authorities who chose to put a child on a plane without notifying any of his family members, including those who had been waiting in the United States to take the boy into their home.

“I’m not going to tell you that we were going to shower him with riches,” Mr. Rodríguez said. “We’re poor, but we were going to fight to support him. We were going to welcome him like he deserved.”

Kirk Semple contributed reporting.