Major air traffic control staffing shortages snarled thousands of flights on Saturday as the government shutdown caused mounting travel woes and raised alarm among airline officials.

The Federal Aviation Administration said there were air traffic control staffing issues affecting 42 airport towers and other centres and delaying flights in at least 12 major US cities—including Atlanta, Newark, San Francisco, Chicago, and New York. Flights crossing six different high-traffic areas were also facing delays.

Some 1,500 flights were cancelled and 6,000 flights were delayed on Saturday, compared with Friday when 1,025 were cancelled and 7,000 were delayed.

Airline officials privately said the number of delay programs made it nearly impossible to schedule and plan many flights and expressed alarm about how the system would function if staffing issues worsen.

Flight reductions to increase on Tuesday

The FAA instructed airlines to cut 4% of daily flights starting on Friday at 40 major airports because of air traffic control safety concerns. The shutdown, which has reached a record 39 days, has led to shortages of air traffic controllers who, like other federal employees, have not been paid for weeks.

Reductions in flights are mandated to rise to 6% on Tuesday and then hit 10% by November 14.

The air traffic absences prompted the FAA to impose ground delay programs at nine airports on Saturday, with delays averaging 282 minutes for flights at Atlanta, one of the busiest US airports.

The cuts, which began on Friday morning, include about 700 flights from the four largest carriers: American Airlines, Delta Air Lines, Southwest Airlines, and United Airlines.

The four airlines canceled about the same number of flights on Saturday, under the FAA mandate, but were forced to cancel additional flights due to air traffic control staffing issues.

Earlier this week, FAA Administrator Bryan Bedford said 20% to 40% of controllers had not been showing up for work over the previous several days.

During a US Senate debate on Friday, Senator Ted Cruz blamed the shutdown for air traffic control concerns. Cruz, a Texas Republican who chairs the Senate Commerce Committee, said he has been told that since the shutdown started, pilots have filed more than 500 voluntary safety reports about mistakes made by air traffic controllers because of fatigue.

Talks to end shutdown look positive

Senate Majority Leader John Thune said on Saturday that bipartisan talks to end the shutdown had taken a positive turn, but the workday ended with no deals announced. The Senate is to try again with a rare Sunday session.

During the government shutdown, 13,000 air traffic controllers and 50,000 security screeners have been forced to work without pay, leading to increased absenteeism. Many air traffic controllers were notified on Thursday that they would receive no compensation for a second consecutive pay period next week.

US Transportation Secretary Sean Duffy said it was possible he could require 20% cuts in air traffic if more controllers stop showing up for work. “I assess the data,” Duffy said. “We're going to make decisions based on what we see in the airspace.”

The Trump administration has cited air traffic control problems as Republicans try to pressure Senate Democrats to back what they call a “clean” government funding bill with no strings attached. Democrats blame the shutdown on a Republican refusal to negotiate over health insurance subsidies that will expire at the end of this year.