A federal judge ordered the Trump administration on Thursday to retract directives that prompted the firing of thousands of federal workers, saying that those directives were “illegal” and suggesting that the layoffs be stopped.

The ruling, by Judge William Alsup of the Northern District of California, stopped short of ordering a halt in the firings and added to the confusion for federal employees, who have been rattled by the mass firings in recent days.

But Judge Alsup found that the government’s human resources division had exceeded its authority when it issued a pair of memos outlining steps to fire an estimated 200,000 probationary workers.

That division, the Office of Personnel Management, is meant to guide agencies but not order them to take action, he said. But government agencies responded to the O.P.M. memos with sweeping firings, a first step in the drastic overhaul of the federal bureaucracy President Trump promised to carry out alongside Elon Musk, a top adviser.

Judge Alsup’s ruling came in a lawsuit filed by several labor unions, including the A.F.L.-C.I.O. and the American Federation of Government Employees, contesting the firings of thousands of probationary workers.

Judge Alsup said the government must quickly alert the agencies whose employees were involved in the lawsuit — including the National Park Service, the Bureau of Land Management and the National Science Foundation — of his finding that directives were illegal. He also ordered that the Pentagon be notified, despite it not being party to the lawsuit, expressing concern over news reports that firings there were imminent.

He indicated that while he did not believe he had the power to grant a more expansive restraining order requiring agencies to halt planned layoffs, he expected them to comply with the spirit of the law, based on his finding that any firings done at the urging of O.P.M. were unlawful.

“I am going to count on the government to do the right thing and to go a little bit further than I have ordered and to let some of these agencies know what I have ruled,” he said in his ruling from the bench.

The judge’s decision was limited to the agencies and offices that employ workers represented by a coalition of unions that had brought the lawsuit.

Judge Alsup, appointed by President Bill Clinton, said many agency heads had indicated publicly and in internal notes to staff that they had taken the office’s memos as an order. But he said he could not stop agencies from independently firing workers.

Nonetheless, the coalition of unions behind the lawsuit celebrated the ruling.

“These are rank-and-file workers who joined the federal government to make a difference in their communities, only to be suddenly terminated due to this administration’s disdain for federal employees and desire to privatize their work,” Everett Kelley, the national president of the American Federation of Government Employees, said in a statement. “O.P.M.’s direction to agencies to engage in the indiscriminate firing of federal probationary employees is illegal, plain and simple.”

While he said that he viewed the O.P.M.’s actions in recent weeks as broadly illegal, he nonetheless noted that agencies could make personnel changes on their own, which could include terminating probationary workers, depending on the justification for the move.

“Congress has given the authority to hire and fire to the agencies themselves,” he said.

“The agencies can thumb their nose at O.P.M. if they wanted to — if it’s guidance,” he said. “But if it’s an order, or cast as an order, then the agencies may think they have to comply, even though I’m telling them right now: They don’t.”

Judge Alsup called probationary workers the “lifeblood” of the federal work force, saying that moves to fire them en masse harmed agencies and sapped the expertise of young workers and recent graduates.

He also said he would set a date for an evidentiary hearing next month in which Charles Ezell, the acting director of the O.P.M., would be summoned to testify under oath about the memos his office had sent out.

• This article originally appeared in The New York Times.