The U.S. currency - all $100 bills - was reported missing on Monday after a count of the money at the Federal Reserve came up short.
The shipment had arrived at John F. Kennedy International Airport on Saturday afternoon aboard a Swiss International Air Lines flight, said FBI spokesman J. Peter Donald. The FBI is investigating whether the cash disappeared from a cargo hold in Zurich, where Flight 17 originated, or sometime after it landed.
The JFK airport's operator, the Port Authority of New York and New Jersey, declined to comment on Tuesday.
In an email, the airline also said it could not comment due to the ongoing investigation. But it added it had "no indication that any valuables were removed from a Swiss International Air Lines aircraft" at JFK.