A federal court on Friday upended a central pillar of the Trump administration’s immigration agenda, ruling that asylum-seekers must be allowed into the country while their cases weave through US immigration courts.

A three-judge panel of the US Court of Appeals for the Ninth Circuit in San Francisco blocked a policy that has required people applying for asylum at the border to wait in Mexico while their claims are reviewed, a process that often takes months or years.

Since the new restrictions were rolled out early in 2019, more than 59,000 asylum-seekers have been turned back by US authorities into Mexican border cities, where kidnappings and violence have surged. Because shelters in Mexico are scant and overrun, many of the migrants are living in vast tent encampments exposed to the elements. Powerful Mexican drug cartels have moved in to exploit them.

“It’s a resounding rejection,’’ said Judy Rabinovitz of the American Civil Liberties Union, who was the lead attorney representing the plaintiffs. She added, “The policy is a disgrace, it’s illegal, it’s morally indefensible, and it needs to stop.’’

The policy the court reviewed is known formally as “migrant protection protocols’’ — though the lawyers who challenged it argued that it did just the opposite by placing vulnerable people in harm’s way. Instead of safeguarding people fleeing persecution abroad, as is required under federal law, the policy merely banished them to perilous conditions in a different place, the lawyers argued.

In their opinion Friday, the judges said the policy is “invalid in its entirety’’ and concluded that a lower court ruling that initially enjoined its implementation was “not an abuse of discretion.’’

Often known as “Remain in Mexico,’’ the policy is part of a constellation of measures undertaken by the Trump administration to help stem the record number of migrant families, mainly from Central America, who began crossing the border in the fall of 2018.

The influx led to overcrowded detention facilities and overwhelmed immigration courts, prompting President Trump to double down on his pledges to build a wall and clamp down on immigration across the border.

In a separate ruling Friday, the same panel of appeals court judges rejected another of the Trump administration’s attempts to restrict asylum. In that case, the judges reviewed a policy that blocks anyone who had entered the United States illegally — as opposed to presenting themselves at a legal port of entry — from applying for asylum.

The court found that the policy runs counter to asylum law, which states that people can apply for the status regardless of where they enter the country. That policy had been enjoined shortly after it was announced, and the appeals court judges on Friday reaffirmed the injunction.

“What’s especially significant is that, in both cases, the court found that the administration ignored Congress,’’ said Lee Gelernt, deputy director of the ACLU’s immigrants’ rights project, who argued the case.

The administration took additional steps last year to make it harder to apply for asylum, signing a deal with Guatemala to resettle asylum-seekers there, instead of in the United States. It also adopted a policy requiring most applicants from Central America to seek asylum first in at least one other country along their route of travel.

That policy is also being challenged in federal court, but together, the various policies have effectively shrunk the US asylum system to a fraction of what it once was. By the end of the 2019 fiscal year, in October, overall border apprehensions had shrunk to 60,781, from a high of 144,116 in May.

Those who are waiting in Mexico now face more aggressive policing by Mexican authorities, who have been cracking down on migrants under pressure from Trump, as well as additional legal hurdles in the United States, which they are allowed to enter only for immigration court hearings.

“On every level, it’s the opposite of protecting people,’’ said Karen Musalo, a lawyer and professor at the University of California, Hastings law school who helped argue the case, along with the ACLU and other advocacy groups.

Government lawyers may quickly move to reverse the decision, before border agents are once again overwhelmed by thousands of people who must now be processed and allowed into the United States. They could request an immediate stay, or an “en banc’’ review by all of the judges on the Ninth Circuit — once a reliably progressive venue that has seen a number of recent conservative appointees. Another option would be to request that the case be taken up by the Supreme Court, where Trump has secured a conservative majority.

Lawyers who brought the challenge were representing a group of 11 asylum-seekers who had been returned to Mexico and several legal advocacy organizations. They filed the case in February, a month after “Remain in Mexico’’ was first implemented in San Ysidro, Calif.

The plaintiffs won a nationwide injunction, but because a higher court stayed the ruling, the policy has continued to expand — most recently taking effect in Nogales, Ariz., in December.

Hundreds of asylum-seekers subject to it have given up their claims, accepting free transportation provided by the US government and the United Nations back to their homes in Central America.