President Trump’s executive order freezing most U.S. foreign aid for 90 days has thrown into turmoil programs that fight starvation and deadly diseases, run clinical trials and seek to provide shelter for millions of displaced people across the globe.

The government’s lead agency for delivering humanitarian aid, the U.S. Agency for International Development, or U.S.A.I.D., has been hit the hardest. Mr. Trump has accused the agency of rampant corruption and fraud, without providing evidence.

The Trump administration ordered thousands of the agency’s workers to return to the United States from overseas; put all of the agency’s direct hires, including its roster of Foreign Service officers, on indefinite administrative leave; and shifted oversight of the agency to the State Department.

On Thursday, the Trump administration announced plans to gut the agency’s staff, reducing U.S.A.I.D.’s work force of more than 10,000 to perhaps a few hundred. On Friday, a judge temporarily blocked elements of the Trump administration’s plan to shut down the agency, though the aid freeze remains in effect.

Critics say Mr. Trump’s executive order will cause a humanitarian catastrophe and undermine America’s influence, reliability and global standing.