FlightAware, a flight tracking website, said by Monday morning, more than 1550 flights had been cancelled and 1400 delayed.
This followed almost 3000 cancellations and nearly 10,800 delays on Sunday, in the single worst day for flight disruptions since the government shutdown began on October 1.
A November winter storm in Chicago is also disrupting air travel.
The Federal Aviation Administration late Sunday said it was suspending general aviation traffic at 12 airports with air traffic control staffing issues, including Chicago O'Hare and Reagan Washington National.
The shutdown, which has reached a record 40 days, has led to shortages of air traffic controllers who, like other federal employees, have not been paid for weeks.
The US Senate voted to advance a bill to end the government shutdown late on Sunday.
In a procedural vote, senators advanced a House-passed bill that will be amended to fund the government until January 30 and include a package of three full-year appropriations bills.
If the Senate eventually passes the amended bill, the package still must be approved by the House of Representatives and sent to President Donald Trump for his signature, a process that could take several days.
The Federal Aviation Administration instructed airlines to cut four per cent of daily flights starting on Friday at 40 major airports because of air traffic control safety concerns.
Reductions in flights are mandated to reach six per cent on Tuesday and then hit 10 per cent by November 14.
One big question for airlines is when the FAA will lift the government-required flight cuts.
Transportation Secretary Sean Duffy has said he first wants to see air traffic control staffing and safety data improve.
