The absence of controllers on Friday is by far the most widespread since the shutdown began, with one of the worst-hit regions being New York, where 80% of air traffic controllers were out, the agency said.
At least 35 FAA facilities, including several at the largest US airports, reported staffing problems.
Airports affected included facilities in New York, Austin, Newark, Phoenix, Washington, Nashville, Dallas and Denver.
At some airports, delays averaged one hour or more.
The shutdown has forced 13,000 air traffic controllers and 50,000 Transportation Security Administration officers to work without pay.
“After 31 days without pay, air traffic controllers are under immense stress and fatigue,” the FAA said late Friday.
“The shutdown must end so that these controllers receive the pay they’ve earned and travelers can avoid further disruptions and delays,” it added.
The impact on the system would have been far worse on a typical Friday.
However, Halloween evening traffic was 20% lower than usual, which helped mitigate the effects of staffing shortages, airline officials said.
More than 5,600 flights were delayed on Friday and 500 cancelled, according to FlightAware, a flight tracking website.
At New York’s LaGuardia Airport, 50% of flights were delayed and 12% canceled, with delays averaging 140 minutes, while Washington, DC’s Reagan National Airport had a quarter of flights delayed.
Airlines are bracing for more flight disruptions.
“Coming into this weekend and then the week after, I think you are going to see even more disruptions in the airspace,” US transportation secretary Sean Duffy said on Fox News’ “America’s Newsroom”.
Calls for ‘continuing resolution’
On Thursday, air traffic control staffing shortages snarled flights at Orlando, Dallas/Fort Worth and Washington, DC, when FlightAware data showed 7,300 flights delayed and 1,250 canceled across the US.
Delta Air Lines, United Airlines, Southwest Airlines and American Airlines have all called on Congress to quickly pass a stop-gap funding bill known as a “continuing resolution” to let the government reopen amid talks on disputes over healthcare policy.
National Air Traffic Controllers Association president Nick Daniels on Friday joined the airlines in calling for a continuing resolution.
The government shutdown began on Oct 1 and continued as a federal funding bill has stalled in Congress.
Republican lawmakers want to pass a “clean” funding measure with no strings attached, while Democrats have demanded talks on extending healthcare subsidies set to expire at year-end.
Airlines have repeatedly urged an end to the shutdown, citing aviation safety risks.
The shutdown has exacerbated existing staffing shortages, threatening to cause widespread disruptions similar to those that helped end a 35-day government shutdown in 2019.
The FAA is about 3,500 air traffic controllers short of targeted staffing levels and many had been working mandatory overtime and six-day weeks even before the shutdown.