A 911 caller said "they were going to blow up the Statue of Liberty", the National Park Service said.
Federal police arrived and when sniffer dogs found "an area of interest" near lockers at the statue's base, the island was evacuated.
After a sweep, the area was declared safe by late afternoon.
The city's fire department said it had been called at 12:57 local time (16:57 GMT) for the investigation of "a suspicious package".
Statue Cruises, which takes tourists to the Statue of Liberty National Monument and Ellis Island, said ferries were postponed after officials found a suspicious package at Liberty Island.
Karen Mason, 68, of Cincinnati, Ohio, said they had just boarded a boat at Ellis Island at 12:40 p.m.
"All of a sudden, they said 'Disembark, disembark, disembark. We have to evacuate the boat,'" she said.
There was no sense of danger, she added. "But we saw helicopters and we knew something was going on," she said.
The statue was given to the US by France in 1886, in recognition of the friendship between the two nations.
Hundreds of tourists were evacuated from New York's Statue of Liberty and Liberty Island as a precaution due to a bomb threat and suspicious package.