Port Authority of New York and New Jersey spokeswoman Sara Beth Joren says Terminal A was evacuated for about an hour Wednesday evening.
It's unknown if flights were delayed or canceled because of the shutdown.
Such security shutdowns at the airport are fairly common.
A security checkpoint was briefly closed last month after a Transportation Security Administration officer saw a water bottle in a carry-on bag but the wrong bag was removed for inspection. A checkpoint also briefly closed in February when an improperly screened passenger entered a secure area.
Part of a terminal briefly closed in December when a computer monitor checked as baggage caused a security scare.