A small but worrisome measles outbreak has contributed to the delays, causing a halt in evacuation flights as federal officials scramble to contain cases and inoculate new arrivals against the disease and other illnesses, including the coronavirus.

As of Sept. 14, about 64,000 evacuees from Afghanistan had arrived in the United States. The vast majority were at risk under Taliban rule after the U.S. withdrawal from the country last month. Nearly 49,000 are living on eight domestic military bases, waiting to be resettled in the United States, according to an internal federal document obtained by The New York Times. Roughly 18,000 are on bases overseas, largely in Germany. Some leave within weeks, but most stay longer.

The screenings, which involve an array of federal agencies, follow a condensed and harried evacuation effort last month shortly before the United States completed its withdrawal from Afghanistan. About 100 Americans who want to leave, and an unknown number of vulnerable Afghans, remain in the country.