(CNN) -- Of the 28,000 commercial airline flights that take to the skies on an average day in the United States, fewer than 1 percent are protected by on-board, armed federal air marshals, a nationwide CNN investigation has found.

An air marshal, far left, trains during a simulated hijacking days after the 9/11 attacks.

That means a terrorist or other criminal bent on taking over an aircraft would be confronted by a trained air marshal on as few as 280 daily flights, according to more than a dozen federal air marshals and pilots interviewed by CNN.

The Transportation Security Administration flatly denied those reports.

Greg Alter, assistant special agent in charge of the federal air marshal program, said the 280 number "grossly understates coverage by an order of magnitude" and that the number is "four digits," but he would not elaborate.

In a post on its Web site responding to the CNN story, the TSA said it would not disclose the number of air marshals flying each day so as not to "tip our hand to terrorists." However, it said, "The actual number of flights that air marshals cover is thousands per day." Read the full response

The investigation found low numbers even as the TSA in recent months has conducted tests in which it has been able to smuggle guns and bomb-making materials past airport security screeners.

The air marshal program began in 1970, after a rash of airline hijackings, and it was expanded significantly after the terrorist attacks of September 11, 2001. Specially trained to safeguard passengers and crew aboard crowded aircraft, air marshals were seen as a critical component in the overall effort to secure America's commercial aviation system.

One pilot who crisscrosses the country and flies internationally told CNN he hasn't seen an air marshal on board one of his flights in six months. A federal law enforcement officer, who is not affiliated with the air marshal service and who travels in and out of Washington every week, said he has gone for months without seeing a marshal on board.

Neither individual wanted to be identified because neither is authorized by his employer to speak.

Yet another pilot, who wanted to protect his identity because he carries a weapon in the cockpit, said he regularly flies in and out of New York's airports and almost never encounters an air marshal.

"I would have to guess it's fewer than 1 percent of all my flights," the pilot said. "I'm guessing by the coverage of when I go to those cities, fewer than 1 percent."

Air marshals who spoke with CNN anonymously in order to protect their jobs are especially troubled by the lack of coverage on flights in and out of Washington and New York, the two cities targeted by the 9/11 hijackers. Marshals, pilots and other law enforcement officials told CNN these flights are protected by far fewer air marshals than in the past. Watch an air marshal reveal the "truth" he says is being hidden from the public »

The TSA refuses to release either the total number of marshals regularly assigned to flights or a percentage of daily flights that are covered, but called the numbers given to CNN "a myth."

Alter denied CNN an on-camera interview with Dana Brown, director of the Federal Air Marshal Service.

"Since the Federal Air Marshal Service post-September 11, 2001, expansion, the volume of risk-based deployments has consistently remained at, near or exceeded target levels," Alter wrote in an e-mail to CNN. He added, "Today, many thousands of dedicated and highly trained Federal Air Marshal Service [sic] work diligently around the globe to make air travel safer than it's ever been."

But Alter did not specify what those target levels are, and those inside the marshals service say there are nowhere near "thousands" of air marshals working the skies.

Air marshals told CNN that while the TSA tells the public it cannot divulge numbers because they are classified, the agency tells its own agents that at least 5 percent of all flights are covered.

But marshals across the country -- all of whom spoke with CNN on the condition they not be identified for fear of losing their jobs -- said the 5 percent figure quoted to them by their TSA bosses is not possible.

One marshal said that while security is certainly one reason the numbers are kept secret, he believes the agency simply doesn't want taxpayers to know the truth.

"I would be very embarrassed by [the numbers] if they were to get out," one air marshal said.

"The American public would be shocked. ... I think the average person understands there's no physical way to protect every single flight everywhere," the air marshal said. "But it's such a small percentage. It's just very aggravating for us."

Sources inside the air marshal field offices told CNN the program has been unable to stem the losses of trained air marshals since the program's numbers peaked in 2003 -- and many of those who have left have not been replaced. Read how Drew Griffin got the story

CNN was told that staffing in Dallas, Texas, for instance, is down 44 percent from its high, while Seattle, Washington, has 40 percent fewer agents. Las Vegas, Nevada, which had as many as 245 air marshals, this past February had only 47.

The Transportation Security Administration is advertising for applicants to fill 50 air marshal positions.

Federal Air Marshals Deployed to detect, deter and defeat hostile acts

Blend in with passengers to protect the flying public

Trained in firearms and recognizing terrorist behavior

Learn special tactics for use during flights

Source: Transportation Security Administration

The decline in the number of air marshals comes as no surprise to pilots. David Mackett, president of the Airline Pilots Security Alliance and a pilot himself, said that, based on conversations with other pilots and marshals, he believes the TSA is overstating the number of flights that are protected by a federal marshal.

In his e-mail to CNN, Alter wrote, "In 2007, the Federal Air Marshal Service attrition rate was approximately 6.5 percent, the same approximate average it has been for almost the entire period since the agency's expansion after September 11, 2001."

"I can only speak for myself and the 23,000 members of my organization, and we are not seeing anywhere near the coverage they are asserting they have," Mackett said. "They are whistling past the graveyard, hoping against hope that this house of cards that they call airline security doesn't come crashing down around them."

As it turns out, the words "coverage" or "covered" have special meaning when applied to the air marshal service. In his e-mail to CNN, TSA's Alter said, "The Federal Air Marshal Service employs an intelligence driven and risk based approach to covering flights."

In a phone conversation with correspondent Drew Griffin, Alter said he uses the term "covered" to mean that a federal marshal is on board. But air marshals and pilots CNN spoke with say that's not exactly the case.

These sources say the marshal service considers a flight "covered" even if a marshal is not on board -- as long as a law enforcement officer or pilot in possession of a firearm is on board, even if that person is flying for personal reasons. The "covered" designation includes pilots armed in the cockpit.

"Yes, they've specifically told us that we're a covered flight when there's an armed, trained person on the plane, then that's a covered flight," said the pilot who regularly flies in and out of New York and who is trained under a federal program to carry a weapon in the cockpit.

The firearms training program for pilots is budgeted at $25 million. And while it is popular among airline pilots, many complain that they have to spend as much as $3,000 of their own money for lodging and meals when they take the course.

By comparison, the federal air marshal budget this year is $720 million. But air marshals who spoke with CNN question where the money is going when their numbers are dwindling and fewer than 1 percent of flights are covered on any given day.

"I'm afraid in the past, the only things that have really worked has been to call out the media and say we need people to call their congressman, call their senators and tell them they want better protection, and hopefully the changes will trickle down to us," one marshal said.

Critics also ask whether our government is doing enough to protect the public if the number of marshals protecting planes is down and screeners aren't catching weapons in controlled tests. Former Rep. Tim Roemer, D-Indiana, voted against the creation of the Department of Homeland Security, the bureaucracy that oversees the federal air marshal service under the auspices of the TSA. He also served on the 9/11 commission that investigated the terrorist attacks.

"This is an agency or department that is critical for the U.S. long-term security needs," Roemer said. "So the basic building blocks, the front line of defense are air marshals. If you're not providing that safety for our people on a pretty basic program seven years after 9/11, we've got a lot of work to do at the department, and probably Congress has a lot more work to do on its oversight." E-mail to a friend

This is an exclusive report from the CNN Special Investigations Unit.

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