SAN FRANCISCO — An appeals court on Friday refused to freeze a California-based judge’s order halting the Trump administration from downsizing the federal workforce, which means that the Department of Government Efficiency-led cuts remain on pause for now.

A split three-judge panel of the U.S. 9th Circuit Court of Appeals found that the downsizing could have significant ripple effects on everything from the nation’s food-safety system to veteran health care, and should stay on hold while a lawsuit plays out.

The judge who dissented, however, said President Donald Trump likely does have the legal authority to downsize the executive branch and there is a separate process for workers to appeal.

The Republican administration had sought an emergency stay of an injunction issued by U.S. Judge Susan Illston of San Francisco in a lawsuit brought by labor unions and cities, including San Francisco and Chicago, and the group Democracy Forward.

The Justice Department has also previously appealed her ruling to the Supreme Court, one of a string of emergency appeals arguing federal judges had overstepped their authority.

The judge’s order questioned whether Trump’s administration was acting lawfully in trying to pare the federal workforce.

Trump has repeatedly said voters gave him a mandate to remake the federal government, and he tapped billionaire Elon Musk to lead the charge through the Department of Government Efficiency.

Tens of thousands of federal workers have been fired, have left their jobs via deferred resignation programs, or have been placed on leave. There is no official figure for the job cuts, but at least 75,000 federal employees took deferred resignation, and thousands of probationary workers have already been let go.

Illston’s order directs numerous federal agencies to halt acting on the president’s workforce executive order signed in February and a subsequent memo issued by DOGE and the Office of Personnel Management.

Illston, who was nominated to the bench by former President Bill Clinton, a Democrat, wrote in her ruling that presidents can make large-scale overhauls of federal agencies, but only with the cooperation of Congress.

Lawyers for the government say that the executive order and memo calling for large-scale personnel reductions and reorganization plans provided only general principles that agencies should follow in exercising their own decision-making process.

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Associated Press writer Lindsay Whitehurst in Washington contributed to this story.