The employees, in the FAA's Airports Division, work on such things as airport-improvement planning, engineering projects and NextGen, the project to modernize the air-traffic control system by using satellites to guide airplanes.
FAA air traffic controllers, who are considered essential operational employees, aren't affected by the funding dispute.
The 16 Garden City workers, and another 15 in the FAA's regional office in Jamaica, Queens, could be out of work beginning Saturday. The current FAA reauthorization funding expires Friday at midnight, an FAA official said Thursday.
Transportation Secretary Ray LaHood said in a statement Thursday that about 4,000 FAA employees nationwide could be furloughed unless Congress acts.
"Congress needs to stop playing games," LaHood said. "There's no excuse for not getting this done."
Long-term funding authority for the FAA expired in 2007. Congress has been unable to agree on long-term funding since then but has kept the FAA operating with 20 short-term, stopgap funding measures.
Usually, the FAA funding is uneventful. However, this time House Republicans added a provision to eliminate government subsidies for airline service to 13 rural communities.
That was unacceptable to Senate Democrats, but House Republicans have been unwilling to remove it.