A Homeland Security K-9 unit was checking into an unattended bag at about 8:30 a.m. EDT (1230 GMT) in the departure area of Terminal Five, said Joe Pentangelo, a spokesman for the Port Authority of New York and New Jersey, which oversees the airport.
Pentangelo said the bomb squad had responded and roadways to the area were temporarily closed. The package was cleared and the terminal resumed normal operations, the spokesman said.
The evacuation came a day after suicide bombers blew themselves up at the main airport in Istanbul, Turkey, killing at least 41 people and injuring hundreds.
After the attack, the Port Authority deployed armed, high-visibility patrols at the three main airports in the New York metropolitan region.