A federal judge in San Francisco on Friday stopped Secretary of State Marco Rubio from proceeding with plans to downsize the State Department, saying that it was prohibited behavior under an injunction she issued last month.

U.S. District Judge Susan Illston barred the Republican administration from carrying out much of its plans to reorganize and slash departments while she hears a legal challenge brought by labor unions and others. She said that President Donald Trump had failed to seek Congressional cooperation to do so when he ordered government-wide cuts.

But, in late May, the State Department notified Congress of an updated reorganization of the agency that would cut programs and personnel even more deeply than previously revealed.

Rubio this week also ordered U.S. embassies to fire all remaining staffers with the U.S. Agency for International Development. He said the State Department will take over USAID’s foreign assistance programs by Monday.

The Trump administration said Rubio had launched a reorganization of the State Department independently of the president’s directive and so was exempt.

Illston, who was nominated to the bench by former President Bill Clinton, a Democrat, was not convinced.

“If the State Department has any question about whether planned actions fall within the scope of the Court’s injunction, the Court ORDERS the Department to first raise those questions with the Court before taking action,” she wrote in an order issued Friday.