The secretary, Robert L. Wilkie, has no experience in emergency management, and he has been largely absent from public briefings with senior officials on the pandemic. “Secretary Wilkie has attended 20 coronavirus task force meetings since he joined the task force on March 3,” said Christina Mandreucci, a spokeswoman for the department. Mr. Wilkie recently fired his second in command, who had worked in past disasters, and his head of emergency preparedness retired.

Senior officials in the department say they are kept out of the loop on major decisions, such as whether it will continue Mr. Trump’s preferred policy of sending veterans into the community for care, and learn from the news media about how centers are interpreting guidelines.

Many of the newcomers in agencies lack relationships with the private sector and lawmakers to accomplish basic goals.

One high-profile case came with eliminating a directorate at the White House’s National Security Council that was charged with pandemic preparations. In 2018, John R. Bolton, then Mr. Trump’s national security adviser, ousted Thomas P. Bossert, Mr. Trump’s homeland security adviser and longtime disaster expert. The directorate was folded into an office dedicated to weapons of mass destruction.

Equally notable may have been the resignation last year of Scott Gottlieb, the commissioner of the Food and Drug Administration, who was an early advocate for broad coronavirus testing and stronger mitigation policies. He was succeeded by Dr. Stephen M. Hahn, a noted oncologist, who has struggled during Senate hearings to explain some of his positions. The agency is largely viewed as slow in engaging the private sector to develop tests for the coronavirus. Many members of Mr. Gottlieb’s team departed with him, leaving the agency with many people new to their jobs.

The Department of Homeland Security, the agency tasked with screening at airports and carrying out the travel restrictions that were Mr. Trump’s first major action to combat the coronavirus, is full of vacancies. Of the 75 senior positions listed on the department’s website, 20 are either vacant or filled by acting officials.