Once federal officials have scrutinized those airports' security measures, they will then look into smaller commercial airports.
"We decided it would be worthwhile to look at the issue of access to non-public areas of airports on a broader scale," FAA spokesman Eliot Brenner said Wednesday.
The agency will also determine whether it needs to do "red team testing," such as sending undercover agents to try to penetrate security to ensure that identified problem areas have been addressed after the review.
The new security crackdown comes in the wake of tests by federal agents working for the Department of Transportation's inspector general, which targeted four major U.S. airports in Miami, Salt Lake City, San Francisco and Honolulu.
Security at Miami International Airport has not improved over the past ten years, reports Jim Bergamo, of CBS Station WFOR.
The mission for federal agents was to crack the security system designed to keep intruders off America's airplanes. Frighteningly, the agents accomplished their mission dozens of times, reports CBS News Correspondent Bob Orr.
Without displaying identification, agents sneaked through supposedly secure doors and entered off-limit airport areas 46 times. On 51 occasions, they boarded jetliners without being challenged.
"In a high percentage of tests involving airport-access controls, our successful penetration of secure areas almost always resulted in our boarding an aircraft," said Alexis Stefani, the Transportation Department's deputy assistant inspector general for aviation.
Stefani told lawmakers many of the problems found in a similar audit in 1993 still exist. For example, Stefani said, undercover personnel could enter through emergency exits and penetrate air cargo facilities by following airport personnel through access control points.
Stefani attributed the "human element" as the primary weakness in keeping unauthorized personnel out of secured areas.
In turn, the FAA blamed airports, airlines and their employees for a lack of vigilance.
In a stern letter, FAA security chief Cathal Flynn warned airport operators to strengthen security or, "it will be necessary to remove the demonstrated vulnerability by... guarding the individual aircraft."
Aviation analysts don't actually expect the FAA to pay for security guards to stand at every airplane.
In fact, analyst Frank McGuire says perfect security is impossible, and no measure proposed by the FAA would prevent a professional terrorist from infiltrating an airport.
"You know what a real pro would do? Go down to the employment office, get a job at minimum wage, wait three or four months and see where the holes are. And then in his lunchbox one day, walk in with a bomb," McGuire said.
Increasing security would be expenive and could slow down the U.S. aviation system. The question is how much are passengers willing to pay to combat a theoretical threat to America's skies.