The stun gun was found by a JetBlue cleaning crew after the flight that originated in Boston landed in Newark around 10:20 p.m. Friday.
Port Authority police turned the stun gun over to the TSA. The agency is responsible for screening those who boarded the flight.
An FBI spokesman said Monday that it did not appear the stun gun was intended to be used in an attack, but would not detail why investigators think that.
It's not clear who the weapon belonged to or how it got on the plane.
Port Authority spokesman Steve Coleman said there were no indications the stun gun was fired.
JetBlue spokesman Sebastian White said the plane's next flight was slightly delayed.
The Associated Press contributed to this report.