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.

Tettey, who scored a "toe-poke" against Manchester United last month, side-footed home to give Norwich a 1-0 win.
"If I score a goal it will be talked about. Today it was nice to do a Yaya Toure," he told BBC Radio Norfolk.
"I was happy, when I made contact with the ball I looked up and it was just going in, it was a great goal."
Victory at Carrow Road against the Saints was Norwich's third win in their last four Premier League matches and left them 15th in the table, six points clear of the relegation zone.
That followed a run of one win in 11 in all competitions - and the upturn in form has coincided with goalkeeper Declan Rudd coming into the first team for the last six matches.
"For the defenders and Declan as well, he's come into the team and got two clean sheets in a row now," said Tettey.
"For the whole team we are really pleased - where we are, if you're letting in goals you are going somewhere you don't want to be.
"And if you win and don't let in goals you are looking forward - that's what we all want."

The views were expressed following a meeting of the EU Negotiation Joint Ministerial Committee in London.
Mr Davis said the UK government would keep Scotland, Wales and Northern Ireland up-to-date about negotiations.
However, Mr Russell said transparency about UK government plans was needed.
Mr Davis said he wanted to hold a monthly meeting to share analysis as part of a "two-way information flow" with each of the three nations.
He believed that would allow the devolved administrations to voice their views as the Westminster government prepares talks with Brussels.
Mr Davis said: "Today's meeting was an important step in bringing the devolved administrations together with the UK government to discuss how we can work together to get the best deal for the whole of the UK.
"Naturally, there are different standpoints around the table, but the meeting was constructive and amicable. We will meet regularly and share our latest thinking as the UK shapes its negotiating strategy.
"We will work positively with the Scottish government, the Welsh government and the Northern Ireland Executive as we implement the decision of the people of the UK to leave the EU."
Mr Russell said it was "good" that the process of involving the Scottish government was under way.
But he added: "More than four months after the referendum the UK government has still not made its strategic intentions clear.
"There was a discussion over EU market access but we do not know whether UK ministers want to remain inside the single market or the customs union. This will remain a considerable problem as we continue to promote the interests of Scotland.
"The UK Government must provide greater clarity and transparency on its intentions."
He said he made it "absolutely clear" that membership of the single market "is essential for the economic prosperity of Scotland".
The UK government hopes the High Court judgment on how Article 50 will be triggered will be overruled on appeal to the Supreme Court next month.
However, the Scottish government will seek to oppose the UK government in the Supreme Court during the appeal.
The intention is for Lord Advocate James Wolffe, Scotland's most senior law officer, to apply to be heard in the case.
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.
[NEXT_CONCEPT]
Norwich City midfielder Alex Tettey has likened his winner against Southampton on Saturday to those scored by Manchester City's Yaya Toure.
[NEXT_CONCEPT]
The UK's Brexit minister David Davis has hailed his latest talks with devolved ministers but Holyrood's Mike Russell has called for greater clarity on the "strategic objectives".