(Image Credit: Fabrice coffrini/AFP/Getty Images)

More than $1 million was discovered missing from a Swiss Air Lines flight, but whoever took the cash left behind the rest of the loot - another $92 million.

The cash shipment was destined for the Federal Reserve Bank of New York, sources told ABC News today.

"When it got here, the money was missing," FBI spokesman Jim Margolin said. The flight landed at John F. Kennedy International Airport on Monday.

The money disappeared between passenger flight 17's point of origin in Zurich on Saturday and the unloading of the shipping container carrying the stash at New York's international airport about 2:30 p.m. Monday. The money was discovered missing during the official count later Monday at the Fed offices in Lower Manhattan.

Federal Reserve spokesman Jack Gutt said he had no comment on the heist or on the cash shipment.

The missing money was in 12 bundles of $100,000 apiece. It was all $100 bills.

"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."

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."

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 the damaged shipping crate was positioned so the hole was blocked from view until it was removed in New York.

Investigators believe it's most 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.

An official for the Port Authority, which runs New York's airports, said only that it is "an active investigation."

Airline spokeswoman Susanne Mühlemann told 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.

JFK has a long, colorful history of cargo thefts, the most famous being the Lufthansa heist immortalized in Martin Scorsese's 1990 film "Goodfellas."

Three months ago, detectives cracked a long-running operation that saw thousands of packages stolen as they passed through Kennedy Airport's huge U.S. Postal Service mail-processing facilities.