The incident stopped departures for 20 minutes, the FAA said.
It turned out to be a false alarm - no fire.
FAA spokeswoman Kathleen Bergen says a faulty sensor on the tower's 15th floor caused the trouble starting at 5:50 p.m.
She says that the tower was evacuated but that three controllers remained to monitor incoming flights.
Other controllers began to set up a temporary tower atop a terminal.
Departures were held until the sensor was replaced at 6:10 p.m. and operations resumed.
Bergen says four flights were diverted from Newark and landed at other airports but it wasn't immediately known where they went.