In a separate ruling, the appeals court backed a lower court’s preliminary injunction against the administration’s Migrant Protection Protocol requiring asylum-seekers to remain in Mexico while their cases are adjudicated.

Judge William A. Fletcher argued in an opinion that the policy imperils immigrants in violation of legal protections by exposing them to “targeted discrimination, physical violence, sexual assault, overwhelmed and corrupt law enforcement, lack of food and shelter, and practical obstacles to participation in court proceedings in the United States.”

“Uncontested evidence in the record establishes that non-Mexicans returned to Mexico under the MPP risk substantial harm, even death, while they await adjudication of their applications for asylum,” Fletcher wrote.

However, the 9th Circuit granted an emergency stay request from the government until the court takes further action. The judges also asked challengers to respond to the stay request by Monday.

The asylum fight is one of many fronts on which Democratic state officials have clashed with the Trump administration in court over immigration policy. Numerous state attorneys general, including California Attorney General Xavier Becerra, backed the lawsuit challenging the asylum rule.

White House press secretary Stephanie Grisham said in a statement: "The Ninth Circuit’s decision, another reckless nationwide injunction threatening our constitutional structure, obstructs the Executive Branch from faithfully executing the immigration laws passed by Congress and from protecting American citizens and legal immigrants."

Acting DHS Secretary Chad Wolf said in a statement: "This nationwide injunction is grave and reckless, rewrites the laws passed by Congress, and undermines the U.S. Constitution."

The American Civil Liberties Union’s Judy Rabinovitz, an attorney who argued the appeal, said in a statement that the ruling showed “it’s time for the administration to follow the law and stop putting asylum seekers in harm’s way.”

On Friday night, the Justice Department asked the 9th Circuit to put its ruling on the Migrant Protection Protocols on hold while the administration asks the Supreme Court to take up the issue. Officials, including U.S. Ambassador to Mexico Christopher Landau, warned in court filings that the decision risks causing a surge towards the border of as many as 25,000 migrants returned to Mexico in recent months.

“To start, the sudden reinstatement of the preliminary injunction could prompt a rush on the southern border by the some of the 25,000 or more individuals who are in Mexico under MPP and may now seek immediate entry into this country,” Justice Department lawyers wrote. “Processing such individuals would be massively burdensome on its own. ... The injunction thus threatens massive and irreparable national-security and public-safety concerns.”

“Those concerns are not speculative: Mere hours after this Court ruled today, counsel for aliens subject to MPP started contacting CBP demanding that their clients be admitted to the United States; one counsel demanded that CBP admit 1,000 individuals over a bridge at a port of entry on the southern border,” the DOJ filing added.

Landau wrote in the filing: "The panel's decision, unless stayed, will have an immediate and severely prejudicial impact on the bilateral relationship between the United States and Mexico. Both countries face a severe challenge from uncontrolled flows of third-country migrants through Mexico to the United States."

Of the court's granting of the stay request, Rabinovitz wrote in a statement: "This is a temporary step and does not change the fact that courts have ruled multiple times against this illegal policy. We will continue working to permanently end this unspeakably cruel policy.”

Josh Gerstein contributed to this report.