Federal officials moved the controllers from Westbury, Long Island, on Sunday, but warn that the move may result in some flight delays.
The relocation did not sit well with some of the 17 air traffic controllers who live near the Long Island facility and now have to work out of Philadelphia.
The union said at least a dozen of the air traffic controllers did not want to make the move.
The relocation is supposed to free up traffic demand in the Northeast Corridor amid a shortage of air traffic controllers.
The FAA said the change will make management of the airspace more efficient and allow them to hire and train air traffic controllers more quickly.
The New York facility was operating at about 60% of its target staffing levels.
The agency said the understaffed Long Island control center has the nation's lowest success rate in training new controllers while overseeing one of the busiest, most complicated air spaces in the world.
The FAA said Philadelphia has the capability to handle Newark more efficiently.
Control of Newark airport airspace moves from Westbury, LI to Philadelphia
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