The FAA responded in a statement, saying that since September 11, it has increased security at many air traffic facilities.
The 149 air traffic facilities slated to begin closing on April 7 are all staffed by contract employees who are not FAA staffers.
The agency is also still considering eliminating overnight shifts at 72 air traffic facilities, including some at major airports like Chicago's Midway International and General Mitchell Airport in Milwaukee.
The city's international airport was also closed to flights at one point, and staff began building a temporary control tower, as air traffic facilities were switched to emergency power sources.
More than 863 flight delays were attributable to furlough-related staffing shortages on Wednesday at air traffic facilities in Chicago, New York, Washington, Cleveland, Jacksonville, Los Angeles, Detroit and Dallas, the FAA said.
Each employee will lose one day of work every other week, which will amount to a 10 percent reduction in available controller work hours to staff air traffic facilities on any given day.
The agency said it had no choice but to subject most of its 47, 000 employees, including tower controllers, to periodic furloughs and to close air traffic facilities at small airports with lighter traffic.
The statement points out that many FAA air traffic control facilities are inside airport security areas.
"It is vitally important that the FAA make extra efforts to guard air traffic control facilities because our national security is at stake, " NATCA President John Carr said in a statement.
Doug Church, spokesperson for the union, said there have not been any specific threats against air traffic control facilities since the September 11 terrorist attacks, but the security measures are still needed.
Some aviation experts say the elimination of overnight shifts should have been carried out regardless of the sequester at facilities that don't see enough traffic to justify the expense of staffing towers.
Aviation experts contend that even if intruders were able to access a control tower and disrupt operations, the nation's air traffic control system is designed with multiple back-ups so that other facilities could pick up control of the affected air space.
The plan, approved in 2006 by the City Council under Ms. Quinn's leadership, called for spreading trash facilities throughout the city and replacing trucks with barges and trains to reduce traffic and pollution.
Tower closures would not necessarily result in airport closures, because some aircraft can land without air traffic control help, and those that need controller help can communicate with more distant FAA facilities.
CNN: Airports can make case to keep their control towers open
In a bucolic farming area, one large landholder on prime acreage may suddenly set himself apart from the rest, with industrial facilities on his land that others consider an eyesore, and significant large vehicle traffic going to and fro for many months.
While they clearly can't handle the additional traffic, airports are reluctant to give up the rents and landing fees that keep their runways and facilities in decent shape.
The council said the policy addressed a number of complex issues, including managing the traffic demands of the West End, the availability of resident and visitor parking, and improving loading and waiting facilities.
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