The money was a fraction of a shipment of $93 million in cash destined for the Federal Reserve Bank of New York, three sources told ABC News Tuesday.
"When it got here, the money was missing," FBI spokesman Jim Margolin said.
The money disappeared between Flight 17's point of origin in Zurich on Saturday and the unloading of the shipping container carrying the stash at New York's main airport about 2:30 p.m. Monday. The money was only discovered missing during the official count later Monday at the Fed offices in Lower Manhattan. Flight 17 was a passenger flight.
"Three crates of cash were delivered to JFK," one official said, adding that the crates were transported in a larger shipping container. "The crates remained sealed until yesterday. That's when the seal was broken."
Sources say a forklift operator opened the sealed crate and noticed damage to one of the crates in the form of a puncture from a forklift. It was a hole large enough to put your arm in, he said.
Saying that shipping containers often have gouges in them after years of use, the forklift operator told investigators he didn't think the hole was something that needed to be reported. Under questioning, he acknowledged that the gouge was considerably larger than the norm.
"It was certainly not something made by just a hammer or something," another source said.
The forklift operator also told investigators that that the damaged shipping crate was positioned so the hole was blocked from view until it was removed completely in New York.
The missing money was in 12 bundles of $100,000 apiece. It was all $100 bills.
Airline spokeswoman Susanne Mühlemanntold ABC news, "We do not have any indication of a robbery of a Swiss aircraft." She would not, however, discuss what may or may not have happened at the airports on either side of the flight.
Investigators first said it was likely that the money was taken before the flight by someone who either knew what was in the crates or saw a target of opportunity. They have since backtracked, now believing the theft occurred after flight landed at JFK.
The FBI will administer lie-detector tests to JFK employees Wednesday, and the investigation is expected to take a few more days.