Investigators now believe the theft of $1.2 million from a Swiss Air Lines flight occurred after the plane landed John F. Kennedy International Airport, a source tells ABC News.

The investigation will still take a "couple more days," the source said. "Today will tell the story."

Investigators initially believed the money was taken before the flight took off from Zurich on Saturday by someone who either knew what was in the crates or saw a target of opportunity.

The money disappeared between passenger flight 17-s point from 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, headed for the Federal Reserve Bank, was discovered missing during the official count later Monday at the Fed's warehouse in East Rutherford, N.J.

The FBI will administer lie-detector tests to JFK employees later today.

The money was a fraction of $93 million headed to the New York Federal Reserve. 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 Tuesday, 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.

Fabrice coffrini/AFP/Getty Images