If the FAA said building the tower would improve safety, controller Ambrose says, how can it argue that closing the tower won't hurt safety?

Controllers say closing the towers will eliminate one layer of safety -- the extra set of eyes in the tower -- while contributing to the workload at other FAA towers, which will themselves be affected by furloughs.

The FAA said it will manage the system by reducing volume, not reducing safety. As a result, flights to major cities such as New York, Chicago and San Francisco could experience delays of up to 90 minutes during peak hours when the effects of furloughs are felt later this spring. "Delays in those major airports will ripple across the country," the FAA says.

The most immediate impact will be on non-commercial flights. The 189 contract towers handle approximately 20% of all airport operations nationwide, but less than 2.5% of commercial operations, the FAA says.

Advocates for contract towers argue they are suffering a disproportionate amount of pain.

"The rest of the FAA's budget is getting a 5% haircut; the contract towers are getting a 75% cut, because the FAA is cutting 189 of the 251 contract towers," Spencer Dickerson of the U.S. Contract Tower Association told CNN.