By Shivansh Tiwary

(Reuters) -U.S. airlines were scrambling on Thursday to rejig schedules and fielding a flood of customer queries after the U.S. ordered flight cuts at some of the nation's busiest airports, the latest travel disruption from the prolonged government shutdown.

On Wednesday, Transportation Secretary Sean Duffy said he would order steep cuts citing air traffic control safety risks from the government shutdown.

The shutdown, now the longest in U.S. history, has forced some 13,000 air traffic controllers and 50,000 Transportation Security Administration agents to work without pay.

Staffing shortages have already caused tens of thousands of flight delays nationwide, with airlines estimating that at least 3.2 million travelers have been affected.

Industry sources told Reuters that the first round of reductions, cutting about 4% of scheduled flights, will take effect as soon as Friday. The cuts will rise to 5% on Saturday, 6% on Sunday, and reach as much as 10% by next week if the shutdown persists.

CUTS THREATEN BUSY HOLIDAY TRAVEL

Unless government reopens, the drastic plan threatens to throw holiday plans into chaos for millions of Americans travelling for Thanksgiving, marking one of the most visible ripple effects yet from the record-long government shutdown.

"The longer this goes on, the more disruption there is and fewer the passengers are going to be flying ultimately," said David Morrison, senior market analyst at Trade Nation, UK.

"They (the airlines might) have some flexibility on prices, but if this shutdown goes on much longer then that's should have a negative effect overall."

The Federal Aviation Administration is expected to formally issue the order for flight reductions later on Thursday.

The move aims to ease pressure on controllers, with the FAA short about 3,500 staff and many working mandatory overtime and six-day weeks even before the shutdown.

Airlines including United Airlines , American Airlines and Southwest were inundated with passenger queries on social media platforms like X, as flyers sought clarity on travel plans.

"This will mean lost revenues and a potential hit to profits in what is a highly operationally geared business, where even small changes in the top line can lead to big movements in the bottom line," said Russ Mould, investment director at AJ Bell.

Still, carriers stressed they would try to minimise disruption for customers and rebooking efforts were underway.

United CEO Scott Kirby said the airline will target its cuts on regional flying and non-hub domestic routes and the carrier expects to rebook many affected travelers.

Southwest, the largest domestic carrier, said it is evaluating how the cuts will affect its schedule and it will communicate with customers as soon as possible.

"I guess the good news is that we're in a low-demand period in November," Frontier Airlines CEO Barry Biffle said on Wednesday, adding that the flight reductions could even help the carrier's unit revenue.