Uncertainty and turmoil gripped the U.S. Agency for International Development for a second day, as employees locked out of their offices braced for potential cuts to the work force, while Democrats denounced the Trump administration for what they said was an illegal power grab.

Secretary of State Marco Rubio, who took control of U.S.A.I.D. as its acting administrator on Monday, insisted during a Fox News interview that night that the takeover was “not about getting rid of foreign aid,” and that the goal had been to reform the agency.

“But now we have rank insubordination,” he said, adding that U.S.A.I.D. employees had been “completely uncooperative, so we had no choice but to take dramatic steps to bring this thing under control.”

On Monday night, most senior officials at U.S.A.I.D. received an email from Erica Y. Carr, the acting executive secretary, asking for the “leanest essential personnel numbers” they would need “in order to provide essential services only,” according to a copy viewed by The New York Times. They were given less than an hour to furnish the lists.

The email was the latest sign that Mr. Rubio and Pete Marocco, the State Department’s foreign assistance director whom Mr. Rubio named as his deputy to run day-to-day operations at the agency, plan to drastically scale back the operations of the government’s lead agency for humanitarian aid and international development.

Many of the agency’s senior staff were put on leave last week, after representatives of Elon Musk, the tech magnate whom President Trump has empowered to run a cost-cutting task force, entered headquarters and began to take over its operations. On Saturday, the agency’s two top security officials were put on administrative leave after they tried to prevent Mr. Musk’s representatives from entering secure spaces and getting access to classified materials for which they lacked the proper security clearances.