Bryan Travers, a spokesman for the FBI's Newark office, said information from the investigation so far suggests that no attack was imminent. He would not detail why investigators think that.
The stun gun was found by a crew that was cleaning Flight 1179 from Boston around 10:20 p.m. Friday, after the flight had landed and all 96 passengers were off the plane.
Port Authority of New York and New Jersey police removed the stun gun from the plane and handed it over to the federal Transportation Security Administration, which is responsible for screening passengers.
The investigation, being led by the FBI's office in Boston, is focusing on how the stun gun got onto the plane, Travers said.
"People get caught bring stuff to the checkpoint all the time," he said.
Travers said that by Monday morning it was not clear who may have brought the gun aboard.
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.