US Transportation Secretary Sean Duffy has said that he would order 10% 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, 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," Mr Duffy told reporters, explaining why he made the decision.

While the government did not name the 40 airports affected, the cuts are 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 Airlines 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.