U.S. agents removed the item on Wednesday from the store, called Gotta Have It!
The New York Times says the signed fingerprint card was made at a police station on May 8, 1976. It bears the name John Winston Ono Lennon. At the time, Lennon was applying for citizenship.
Spokesman James Margolin said the FBI is investigating how the item "came to be up for auction."
A store owner, Peter Siegel, said Homeland Security also had inquired about the card.
Siegel said an unidentified concert promoter bought it at a Beatles convention about two decades ago.
Saturday would have been Lennon's 70th birthday.