The shutdown, now in its 36th day and the longest in US history, has forced 13,000 air traffic controllers and 50,000 Transportation Security Administration agents to work without pay. This has worsened staff shortages, caused widespread flight delays and extended lines at airport security screening.
“We had a gut check of what is our job,” Duffy told reporters, explaining why he made the decision.
Reuters earlier reported the plan.
While the government did not name the 40 airports affected, the cuts were expected to hit the 30 busiest airports including those serving New York City, Washington, DC, Chicago, Atlanta, Los Angeles and Dallas. This would reduce as many as 1,800 flights and over 268,000 airline seats, according to aviation analytics firm Cirium.
The move is aimed at taking pressure off air traffic controllers.
The US Federal Aviation Administration also warned that it could add more flight restrictions after Friday if further air traffic issues emerge.
Airlines for America, a trade group representing major US carriers such as Delta, United, American, and Southwest, said its members were trying to understand the next steps.
“We are working with the federal government to understand all details of the new reduction mandate and will strive to mitigate impacts to passengers and shippers,” it said.
The FAA was scheduled to hold a call with airlines on Wednesday evening to explain how the cuts will be implemented, according to industry sources.
The federal government has mostly closed as Republicans and Democrats are locked in a standoff in Congress over a funding bill. Democrats have insisted they would not approve a plan that does not extend health insurance subsidies while Republicans have rejected that.
President Donald Trump and Republicans have been trying to intensify pressure on Democrats by increasing the pain felt by average Americans from the government shutdown.
The closure, which began Oct 1, left many low-income Americans without food assistance, closed many government services and led to the furlough of about 750,000 federal employees.
Duffy had warned on Tuesday that if the federal government shutdown continued another week, it could lead to “mass chaos” and force him to close some of the national airspace to air traffic.
Airlines have repeatedly urged an end to the shutdown, citing aviation safety risks.
Airline stocks dip
Shares of major airlines including United and American were down about 1% in extended trading.
An airline industry group estimated that over 3.2 million passengers have been affected by flight delays or cancellations due to rising air traffic controller absences during the shutdown. Airlines have been raising concerns with lawmakers about the impact on operations.
Airlines said the shutdown has not significantly affected their business but have warned bookings could drop if it drags on. More than 2,100 flights were delayed on Wednesday.
On Tuesday, FAA administrator Bryan Bedford said that 20% to 40% of controllers at the agency’s 30 largest airports were failing to show up for work.
Duffy said the authorities would also limit space launches to certain times of the day.