US Transportation Secretary Sean Duffy said on Wednesday that he would order 10 percent of flights at 40 major US airports to be cut starting on Friday unless a deal to end the federal government shutdown is reached.

The shutdown, which is 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.

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 later 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.

Four sources told Reuters that the FAA told airlines on a call that the planned cuts would start at 4 percent on Friday, rise to 5 percent Saturday and 6 percent on Sunday before hitting 10 percent next week.

The FAA plans to exempt international flights from the cuts but told airlines it was making drastic cuts in general aviation flights at those major airports.

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.

Airlines have repeatedly urged an end to the shutdown, citing aviation safety risks.

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. (Reuters)