In this Oct. 10, 2017, file photo, the Supreme Court in Washington is seen at sunset. The Supreme Court is allowing nationwide enforcement of a new Trump administration rule that prevents most Central American immigrants from seeking asylum in the United States. The justices’ order late Wednesday, Sept. 11, temporarily undoes a lower court ruling that had blocked the new asylum policy in some states along the southern border. Credit: J. Scott Applewhite | AP

WASHINGTON – The Trump administration can begin denying asylum requests from migrants at the southern border who have traveled through Mexico or another country without seeking protection there, after the Supreme Court on Wednesday lifted a lower court’s block on the new restriction.

The justices put on hold an injunction from lower courts in California that halted the new rule pending additional legal action; there, a district judge had said it probably ran afoul of a federal statute and administrative law requirements.

President Donald Trump’s policy is a dramatic change in the way the federal government treats those seeking safe haven in the United States, and is one of the administration’s most significant efforts to deter migrants at the southern border. It is one of multiple tools immigration officials have deployed to prevent entry by families and others fleeing violence and poverty in Central America.

Trump reacted on Twitter: “BIG United States Supreme Court WIN for the Border on Asylum!”

Trump later tweeted Wednesday night that he had “an excellent telephone conversation” with Mexican President Andrés Manuel López Obrador about border security and other issues.

Earlier this summer, the court on a 5-to-4 vote agreed to another emergency request from the administration, allowing it to proceed with plans to use $2.5 billion in Pentagon funds to build part of the president’s wall project along the southern border.

No vote was recorded in the asylum case order, but Justices Sonia Sotomayor and Ruth Bader Ginsburg noted their disapproval of the court’s action in a strongly worded dissent.

“Once again the Executive Branch has issued a rule that seeks to upend longstanding practices regarding refugees who seek shelter from persecution,” Sotomayor wrote.

“Although this Nation has long kept its doors open to refugees – and although the stakes for asylum seekers could not be higher – the Government implemented its rule without first providing the public notice and inviting the public input generally required by law.”

As is common, the court’s majority did not provide a reason for lifting the injunction issued by a lower court. The issue is likely to come back to the Supreme Court when the ongoing legal challenges have been completed in lower courts.

But that could take months, and Sotomayor said the status quo should remain in place until then. The change most affects Hondurans, Salvadorans and Guatemalans leaving behind gang violence and high levels of crime in their countries. It could also turn away migrants fleeing oppressive regimes in Nicaragua, Venezuela and elsewhere.

U.S. Citizenship and Immigration Services acting director Kenneth Cuccinelli tweeted that the Trump administration “uses every tool in the toolbox to try and solve the crisis at our southern border. @USCIS will commence implementing the asylum rule ASAP.”

American Civil Liberties Union lawyer Lee Gelernt stressed that the challenges continue. “This is just a temporary step, and we’re hopeful we’ll prevail at the end of the day,” he said in a statement. “The lives of thousands of families are at stake.”

A record number of Central American families have sought asylum in the United States during the past year, and most have been released to await court hearings, thwarting Trump’s efforts to curb a new wave of migrants. The Justice Department says more than 436,000 pending cases include an asylum application.

The Trump administration announced the change – requiring migrants to seek protection in the first country they travel through – in July.

Four immigrant-rights groups quickly challenged it. A federal district judge in California ruled that the law was probably invalid because it is inconsistent with federal law. He also said it violated the Administrative Procedure Act, and issued a nationwide injunction.

A panel of the U.S. Court of Appeals for the 9th Circuit said the judge went too far. The policy likely violated the APA, it said, but the injunction should be limited to states within the 9th Circuit’s jurisdiction. That meant the rule change could not be implemented along the California and Arizona borders. The other southern border states, New Mexico and Texas, are in different circuits. A U.S. Citizenship and Immigration Services official, who spoke on the condition of anonymity to discuss a sensitive matter, said the new rule has been applied in those border areas.

But U.S. District Judge Jon Tigar on Monday reinstated the nationwide injunction, saying it was the only way to provide the organizations the relief he said they deserved, and to keep the nation’s asylum law uniform.

Even before Tigar’s latest ruling, Solicitor General Noel Francisco had asked the Supreme Court to allow the new rules to be implemented everywhere while the legal battle continued.

Congress gives the departments of Justice and Homeland Security authority to impose additional restrictions on asylum seekers beyond those in federal law, Francisco argued. He said the new requirement “alleviates a crushing burden on the U.S. asylum system by prioritizing asylum seekers who most need asylum in the United States.”

“In turn, the rule deters aliens without a genuine need for asylum from making the arduous and potentially dangerous journey from Central America to the United States,” he added.

The immigrant-rights groups were represented by the ACLU. They called the changes a “blatant end-run around Congress” and a “tectonic change to U.S. asylum law” that should not be allowed without a full briefing on its merits.

“Allowing the ban to go into effect would not only upend four decades of unbroken practice, it would place countless people, including families and unaccompanied children, at grave risk,” Gelernt wrote. The administration’s claim of a crisis at the border “cannot justify ignoring the laws Congress passed.”

Sotomayor seemed to agree. She wrote that “the rule the Government promulgated topples decades of settled asylum practices and affects some of the most vulnerable people in the Western Hemisphere – without affording the public a chance to weigh in.”

She also wrote that she was disturbed that the administration continues to ask the Supreme Court to step in immediately after it receives an adverse ruling in lower courts, rather than allowing the normal legal process to run its course.

She noted a study by University of Texas law professor Stephen Vladeck, which said Francisco’s office “has sought emergency or extraordinary relief from the Supreme Court with unprecedented frequency.”

Sotomayor wrote: “Historically, the Government has made this kind of request rarely; now it does so reflexively.”

The administration counters that no other has had its initiatives thwarted so often by lower courts that enter nationwide injunctions against its policy decisions.

Since 1980, the United States has said that those who say they are fleeing persecution and violence in their home countries have the right to at least apply for asylum.

Michael Knowles, a spokesman for the union that represents asylum officers and other Citizenship and Immigration Services workers, called the new policy “clearly incompatible with the law that says asylum seekers must have their cases heard, irrespective of their method or route of transit.”

Knowles said the ruling will present the asylum officers who interview those seeking protection in a bind. “It’s an ethical and moral dilemma for officers who are tasked with upholding our country’s obligations and laws,” he said. “We believe asylum seekers deserve due process.”

Officers who believe that an asylum seeker would face grave danger if deported to their home country could still potentially refer that person to the immigration court system under the Convention Against Torture, Knowles said. But that person would only be eligible for what is known as “withholding of removal,” a lesser status that blocks their deportation but does not put them on a path to legal U.S. residency.

The current case was the Trump administration’s second attempt to change asylum rules.

In December, the court on a 5-to-4 vote refused to lift a stay on Trump’s first attempt. It would have denied asylum requests from anyone who entered the country at any place other than an authorized “port of entry.”

A different panel of the 9th Circuit said that change was clearly at odds with federal law. Chief Justice John G. Roberts Jr. joined the court’s four liberals in keeping the stay in place while the legal battle continued.

The administration has not yet filed a petition with the Supreme Court to ask it to review the merits of that case.

The new case is Barr v. East Bay Sanctuary Covenant.

The Washington Post’s Nick Miroff contributed to this report.