A federal judge in Washington on Saturday blocked the Trump administration from ousting the top official at a federal watchdog agency, finding that its efforts to do so were unlawful.

In an order on Saturday evening, Judge Amy Berman Jackson granted a permanent injunction against the government, allowing Hampton Dellinger to remain the head of the watchdog agency, the Office of Special Counsel. The order required the Trump administration to recognize Mr. Dellinger’s authority in that position, barring it from taking any action to “treat him in any way as if he has been removed” or otherwise interfere with his work.

The administration immediately indicated it would challenge the ruling, starting an appeals process that appeared likely to end at the Supreme Court.

In a 67-page opinion explaining the order, Judge Jackson, of the U.S. District Court for the District of Columbia, stressed the unique responsibilities Congress gave the office when it was created under a 1978 law. She noted its central role in protecting whistle-blowers in the federal government, a role that she said would be compromised if Mr. Dellinger were allowed to be removed without a cause stipulated under the law. The judge had earlier put a temporary block on the firing.

“It is his independence that qualifies him to watch over the time-tested structure that is supposed to bar executive officials from taking federal jobs from qualified individuals and handing them out to political allies — a system that Congress found intolerable over a century ago,” she wrote.

The ruling came a week after the Supreme Court declined to intervene in the temporary block on removing Mr. Dellinger. Lawyers for the government argued to the court that Mr. Trump had the authority as the head of the executive branch to place his preferred pick in charge of the office.