The federal government will also soon save 10 percent of the supplies on each flight for the national stockpile, according to officials. A Korean War-era production act also allows the federal government to force companies to prioritize its order over another client’s, whether it be a private hospital or another nation.

In the past week, 14 flights carrying more than 83 million gloves, four million masks, one million gowns and 300,000 respirators have landed in New York, Chicago, Miami, Los Angeles, Columbus, Ohio, and Louisville, Ky. Mr. Pence said more than 50 flights had been scheduled.

The administration pivoted to the system of distribution after President Trump tapped FEMA to replace the Department of Health and Human Services as the agency leading the response to the coronavirus pandemic. States had previously submitted formal requests to the government to obtain materials from the stockpile.

Because the federal government determines which states are in greater need, governors and hospitals executives preparing in advance for the worst have complained that FEMA was effectively commandeering their personal protective equipment, or P.P.E.

“FEMA realizes that prioritizing P.P.E. deliveries to Covid hot spots can have the unintended consequence of disrupting the regular supply chain deliveries to other areas of the country that are also preparing for the coronavirus,” said Lizzie Litzow, a FEMA spokeswoman, adding that the agency was not seizing any shipments.

The intervention has confused some local officials and company executives who have watched as the administration has repeatedly called on states to find medical supplies on their own without relying on the federal government. But hundreds of hospitals continue to struggle with widespread shortages of test kits, protective gear for staff members and ventilators, according to a new report by the inspector general for the Department of Health and Human Services.

The chaotic race to procure such supplies has also drawn fraudsters looking to hoard items and resell the equipment at a steep price. A number of F.B.I. investigations are already underway.