Port Authority detectives and FBI agents last night were investigating after $1.2 million in cash was stolen from a Swiss jet that had landed at JFK.

The theft was discovered after the plane arrived yesterday, sources said.

It was not disclosed who the money was meant for or why it was being sent.

But when representatives for the recipient opened the exterior of a cargo container, they found that a smaller receptacle had been emptied, a source familiar with the probe said.

“It’s an active investigation,” a PA police source told The Post last night.

Jim Margolin, a spokesman for the FBI in New York, confirmed that the theft was being investigated, but did not provide further details.

A key element for investigators is their ability to establish exactly where and when the theft took place.

It was not immediately clear if the cash vanished before the jet left its point of departure, which was not disclosed, or if it was stolen after the airplane landed in New York City.

The exterior cargo container — the receptacle holding the smaller container that should have been holding the $1.2 million — showed no signs of being compromised, according to a source familiar with the investigation.

This suggests that the theft might have occurred at the original departure point, the source added

But investigators were also probing whether local mechanics, flight-crew members or other airport personnel had somehow gotten inside the inner container to swipe the dough and then placed the smaller and now-empty cargo container back inside the larger one.

Whoever took the money probably didn’t have too much trouble making off with it.

The weight of $1 million in $100 bills, for example, is estimated at 22 pounds, according to the US Treasury.

The largest cash heist in JFK Airport history occurred on Dec. 11, 1978, when an estimated $5 million was swiped at the Lufthansa Airlines terminal.

It was, at the time, also the largest cash theft on US soil.

That crime was portrayed in the movie “Goodfellas.”

Airlines regularly transport large sums of US cash under “enhanced” security protocols, such as when fulfilling large banking transfers or when vast amounts of American currency are being permanently taken out of circulation prior to destruction.

Those sums can total up to $1 billion or more on a single flight, said a source with direct knowledge of such shipments.