Passengers at Terminal 8, which serves American Airlines, were told to leave for rescreening, the Transport Security Administration said in a statement.
"An individual entered the sterile area in Terminal 8 through a non-public, employee door used by airlines," the TSA said.
"TSA is working closely with the Port Authority to find the individual. The terminal is being evacuated in order to rescreen all passengers to ensure the safety of the traveling public."
The rest of the airport was reported to be unaffected by the incident.
An unauthorized entry of a man into a secure zone at Newark International Airport earlier this month caused huge delays, although he was later found to have just been trying to give a departing passenger a last kiss.
US airports are on high alert after the December 25 attempt by a Nigerian man allegedly to set off a bomb aboard a Northwest Airlines passenger plane.
Keep up with the latest business news from the region with the Emirates Business 24|7 daily newsletter. To subscribe to the newsletter, please click here.