Nearly 500 flights scheduled for Friday were already cut nationwide, and the number of cancellations climbed throughout Thursday afternoon, according to FlightAware, a website that tracks flight disruptions.
The Federal Aviation Administration has ordered airlines to phase in a 10 per cent reduction in their flight schedules across more than two dozen states.
Airlines were scrambling to figure out where to cut, and travellers with plans for the weekend and beyond waited nervously to see if their flights would take off as scheduled.
The affected airports include busy connecting hubs and those in popular tourist destinations, including Atlanta, Denver, Orlando, Miami, and San Francisco. In some of the biggest cities — such as New York, Houston and Chicago — multiple airports will be affected.
"This is going to have a noticeable impact across the US air transportation system," industry analyst Henry Harteveldt said.
The FAA said Wednesday it would reduce air traffic by 10 per cent across "high-volume" markets to maintain travel safety as air traffic controllers exhibit signs of strain during the shutdown.
The controllers have been working unpaid since the shutdown began on October 1, with many calling in sick.
The cuts could affect as many as 1,800 flights, or upward of 268,000 passengers, per day, according to an estimate by aviation analytics firm Cirium.
Package deliveries could also be disrupted because two airports with major distribution centres are on the list — FedEx operates at the airport in Memphis, Tennessee, and UPS in Louisville, Kentucky, the site of this week's deadly cargo plane crash.
Meanwhile, a federal judge has ordered the Trump administration to find the money to fully fund November's SNAP food-aid benefits, which had been suspended after the shutdown.
The ruling gave the government until Friday to make the payments through the Supplemental Nutrition Assistance Program, though it's unlikely the 42 million Americans — about 1 in 8 — will see the money on the debit cards they use for groceries that quickly.
The order was in response to a challenge from cities and non-profits complaining that the administration was only offering to cover 65 per cent of the maximum benefit, a decision that would leave some recipients getting nothing for this month.
US District Judge John J McConnell Jr was one of two judges who ruled last week that the administration could not skip November's benefits entirely because of the federal shutdown.
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