Officials evacuated Terminal 4, Concourse B around 4 p.m. after screeners spotted a suspicious item in a bag.
Just before 5:30 p.m., the suspicious package was cleared and was identified as tape and a toothpaste tube.
Travelers were then let back into the terminal.
Last week, New York's LaGuardia Airport was partially evacuated following a report of suspicious wiring. Ron Marsico of the Port Authority of New York and New Jersey, which runs the airport, says wires protruding from a fluorescent light fixture led someone to call authorities last Tuesday morning. That prompted an evacuation of the upper level of the airport's central terminal building.
The main terminal was partially evacuated at about 10:30 a.m. and reopened about an hour later. New York City is on a heightened security alert as a precaution due to the Monday's bombing at the Boston Marathon.
The Associated Press contributed to this report.