Flights are being severely delayed at La Guardia, Newark, Philadelphia and other airports as a result of the US government shutdown.
Some airports are advising passengers to check with their airline before travelling and to arrive four-five hours early for international flights.
A shortage of air traffic control staff is forcing the FAA to divert flights and increase the spacing between aircraft.
A federal closure, which has been going on since December 21, has left controllers working for more than a month without pay.
As a result, sickness levels have risen, leaving control rooms under staffed.
The FAA issued a statement saying: "We have experienced a slight increase in sick leave at two facilities. We are mitigating the impact by augmenting staffing, rerouting traffic and increasing spacing between aircraft when needed."
Trish Gilbert, executive vice president of The National Air Traffic Controllers Association, a labour union representing controllers, said the system was already under pressure.
She told CNN: "The shutdown has exacerbated an already strained system. You can’t mess with a system that is so integral to the US and its economy. There’s just not going to be enough controllers in our radar rooms across the country."
Reports say there are also delays at other airports across the US, including Washington D.C and Tampa, Florida.
Air traffic controllers, TSA security screeners and others in ‘essential’ roles who have been forced to continue to work unpaid are set to miss a second pay day today (Friday).
Earlier this week, JetBlue CEO Robin Hayes warned that the air travel network is getting close to ‘tipping point’ and said the longer the shutdown continues, the longer it will take for the air travel infrastructure to rebound.
