"If these disruptions unfold as predicted, business travelers will stay home, severely impacting not only the travel industry but the economy overall," the Global Business Travel Association warned the head of the FAA, Michael P. Huerta, in a letter Friday.
Deborah Seymour was one of the first fliers to face the headaches.
She was supposed to fly from Los Angles to Tucson, Ariz., Sunday night. First her 9:55 p.m. flight was delayed four hours. Then at 2 a.m., Southwest Airlines canceled it.
"It's pretty discouraging that Congress can't get it together and now it's reached the point that we can't get on an airplane and fly," Seymour said.
One thing working in fliers' favor Monday was relatively good weather at most of the country's major airports. A few wind gusts in New York added to some delays, but generally there were clear skies and no major storms.
Delta Air Lines said it was "disappointed" in the furloughs and warned travelers Monday to expect delays in the following cities: New York, Philadelphia, Fort Lauderdale, Fla., Chicago, San Francisco, Los Angeles and San Diego.
Many flights heading to Florida were seeing delays of up to an hour.
Raymond Adams, president of the air traffic controllers union at New Jersey's Newark airport, said on Twitter than a few flights out of Newark to the south got sent back to Newark because the Washington area air traffic control system was overwhelmed.
The FAA has also furloughed other critical employees including airline and airport safety inspectors.
The country's airlines and some lawmakers have suggested the White House is causing misery for fliers to put pressure on Republicans in Congress to rescind the cuts. They say the FAA is ignoring other ways to cut its $16 billion budget. Two airline trade associations and the nation's largest pilots union filed a lawsuit Friday asking the U.S. Court of Appeals to halt the furloughs. No hearing date has been set.
In a letter to the FAA Friday, Delta's general counsel Ben Hirst asked the agency to reconsider the furloughs, saying it could make the cuts elsewhere and could transfer funds from "non-safety activities" to support the FAA's "core mission of efficiently managing the nation's airspace."