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.