Sources say the thefts went on for years and the exact amount of stolen cash is expected to be a lot more.
TSA Agents Coumar Persad and Davon Webb are charged with stealing $40,000 from a passenger's bag.
But, a Port Authority Police source says that over several years, the two, acting as a team, took up to $160,000 from checked bags at JFK's American Airline's Terminal.
The source says that one agent would look for the money as bags went through x-ray, and the other would take the cash once the luggage was placed in a baggage room.
"It's ideal for a thief," said Charles Slepian, an aviation expert.
The former head of security for American Airlines says this latest arrest shows the TSA has been slow to come to grips with a widespread theft problem.
"There's no supervision, no procedures, no cameras, if there are cameras, no one is looking at the monitors," Slepian said.
In the past year, Eyewitness News has documented a steady stream of passengers who believe they had valuables taken from their carry-on bags while travelling through New York's three major airports.
"I had inside; right here," said Reiko Anderson of Flushing, Queens.
"Just placed right in there, the wallet," said Jim Hoffer, Eyewitness News Investigative reporter.
Add Hiroshima survivor Reiko Anderson to that growing list.
She contacted Eyewitness News just weeks ago to say she was going through TSA screening at JFK headed for Japan when she realized shortly after that $2,500 in cash had been taken from her wallet.
"At first I refused to think that someone has taken it because these are the people whose job it is to protect the passengers. Security, the safety, so how could these people do these things. But that was the only time that the stuff was out of my sight," Anderson said.
Earlier this week, a TSA Supervisor at Newark Airport admitted to receiving stolen cash that belonged to passengers.
In response to today's arrests, TSA said it has "a zero tolerance policy for theft in the workplace," and called this latest incident "a disgrace".
"If you're looking the other way, you say, 'I have zero tolerance', but you're not seeing what you're supposed to be intolerant of," Slepian said.