WASHINGTON — Mexico has agreed to allow the United States to restart a contentious asylum program that requires certain migrants to wait in Mexico until American immigration officials decide their cases — the latest complication for the Biden administration’s fledgling efforts to remake the country’s immigration system after the restrictive policies of former President Donald J. Trump.
The Biden administration, which announced the agreement on Thursday, has tried to end the program, which American officials and advocacy groups have assailed as dangerous and inhumane. But it has been forced to restart it under a court order, and doing so requires the cooperation of the Mexican government, which had been reluctant to do so without commitments to address humanitarian concerns.
Roberto Velasco Álvarez, head of the North America unit at the Mexican Foreign Ministry, said that Mexico had agreed to the restart of the program, known commonly as Remain in Mexico and formally as Migrant Protection Protocols, after the Biden administration agreed to a number of steps to improve humanitarian conditions at the border, such as providing vaccines for migrants. Unaccompanied minors and other vulnerable asylum seekers will not be included in the program.
“The United States accepted all those concerns and made the modifications to the program accordingly,” Mr. Velasco said.
The Remain in Mexico program will apply to migrants whom the United States is unable to expel under a public health rule it put in place at the beginning of the pandemic.
Ending the program was an early goal for President Biden as he sought to rebuild an asylum system that had largely been dismantled under Mr. Trump. Its resumption creates the challenge of securing cooperation from legal advocates and humanitarian groups, many of whom have already said they would not participate because of ongoing opposition to Mr. Biden’s immigration policies. The Trump administration relied heavily on these groups to assist migrants waiting in Mexico.
Republicans credit the program with curbing illegal migration under Mr. Trump, but critics say it forced migrants to stay in unsanitary tent encampments where they faced sexual assault, kidnapping, torture and harsh weather.
The administration hopes that the groups will change their minds or that new organizations will step in to help, according to an official who spoke on condition of anonymity in order to discuss internal deliberations.
Other changes to the program include limiting immigration proceedings to six months per asylum applicant. During the Trump administration, Remain in Mexico cases sometimes dragged on for years. There are more than 25,000 asylum claims pending from people affected by the program, according to data from the Transactional Records Access Clearinghouse at Syracuse University. Of the cases completed to date, only 1.6 percent of the applicants were granted asylum.
American officials also promised Mexico that they would improve access to counsel for migrants who fear they would be persecuted if they were forced to stay in Mexico while their asylum case was under consideration.
The program’s changes did not satisfy its critics. “This is a disaster waiting to happen,” Aaron Reichlin-Melnick, a policy counsel at the American Immigration Council, wrote in a Twitter post on Thursday.
Alejandro N. Mayorkas, the Homeland Security secretary, has said as much himself.
“I have concluded that there are inherent problems with the program that no amount of resources can sufficiently fix,” he wrote in a justification for ending the program, released at the end of October.
The Trump administration launched the program at the beginning of 2019 as one of several efforts to limit who can seek asylum in the United States.
The Biden administration stopped taking applications for the program the day after Mr. Biden’s inauguration, fulfilling a campaign promise. But Missouri and Texas sued to have it reinstated, and Judge Matthew J. Kacsmaryk of the U.S. District Court for the Northern District of Texas sided with them, ruling in August that the administration’s seven-page justification for ending the program was “arbitrary and capricious.”
The administration appealed, but the Supreme Court in August refused to block the order. The administration then reluctantly took steps to restart the program, the biggest hurdle being whether Mexico would cooperate.
In October, the administration submitted a new, more detailed, justification for ending the program; it has a motion pending in the U.S. Court of Appeals for the Fifth Circuit, in New Orleans. The Department of Homeland Security said Thursday that if the appeals court sides with the administration, it will end the program again immediately.
The program faced court challenges during the Trump administration as well.
Since Mr. Biden has been in office, the United States has seen a spike in the number of migrants — many from Central America — illegally crossing into the United States. The administration has been primarily using an obscure public health rule, known as Title 42, to quickly turn back most such crossers during the pandemic. But for a variety of reasons, it has not been applied across the board.
For example, in October, U.S. officials used the rule just 57 percent of the time to turn away migrants who crossed the border illegally, according to government data.
Of the migrants who were not expelled under the public health order that month, half were from Brazil, Cuba, Nicaragua and Venezuela — countries that typically will not repatriate their citizens.
The resumption of the Remain in Mexico program, beginning on Monday, will add a new option for migrants who cannot be expelled under Title 42.
Mexico’s decision comes the same week that the United States agreed to start a joint development program in Central America that influenced Mexico’s decision, though Mr. Velasco said that “it’s not a quid pro quo.” The program is supposed to address the root causes of migration, beginning in Honduras.
“It’s part of what Mexico has been calling for as well, that cooperation efforts in Central America be accelerated,” he added.
A United States donation of 2.1 million doses of coronavirus vaccine arrived in Mexico on Thursday, bringing the total number of doses sent there by the U.S. government to 13.1 million. Mr. Velasco said the donations had not influenced his country’s decision to go along with restarting the program.
Oscar Lopez reported from Mexico City.