(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.

That means that 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 investigation found those low numbers even as the Transportation Security Administration 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.

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.