Flights at Washington's Dulles International Airport, Reagan National Airport and Baltimore-Washington International Airport (BWI) were among those affected, as well as those at New York's John F Kennedy International Airport and LaGuardia Airport.
Tracking service FlightAware reported that around 400 flights had been delayed or canceled across those airports.
Some flights at BWI were pushed back more than three hours, while a number of travelers at Dulles were told to expect delays of more than an hour.
"Some flights into and out of the New York and Washington, DC metro area airports may be delayed," it added.
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The FAA said is was directing high altitude traffic around the affected airspace.
BWI warned passengers to check with airlines for travel updates as the issue was being handled.
The affected airports are among the country's busiest, especially in the summer holiday months.
The delays had nothing to do with accidents or hacking, an aviation official said.