A judge handed workers across a broad swath of the federal government a reprieve on Thursday night, extending her pause on President Trump’s plans for vast layoffs until a case challenging them is resolved.

The order, issued by Judge Susan Illston of the Federal District Court for the Northern District of California, affects tens of thousands of employees at 22 agencies, including the departments of Housing and Urban Development, State, Treasury and Veterans Affairs. She also ordered the administration not to shut down offices and programs in those agencies, or move them between agencies, as Trump officials have sometimes done in their efforts to dismantle parts of the government.

Workers at those agencies have been bracing for announcements of layoffs for weeks, expecting them to come any day. The planned reorganization is a major component of Mr. Trump’s goal to reshape the federal government.

But Judge Illston said Mr. Trump was not following the laws set by Congress to address such reductions.

“Presidents may set policy priorities for the executive branch, and agency heads may implement them. This much is undisputed,” the judge wrote in her order. “Agencies may not conduct large-scale reorganizations and reductions in force in blatant disregard of Congress’s mandates, and a president may not initiate large-scale executive branch reorganization without partnering with Congress.”

The reprieve is meant to freeze any cuts while Judge Illston fully hears the case and renders a final decision, but it could be much briefer. The administration has already asked the Supreme Court to block the two-week pause that Judge Illston initially issued this month. The court has yet to rule on the emergency application, and the government is expected to request that the justices overturn Judge Illston’s new ruling as well.