Police received reports of possible gunshots at about 9:30pm local time on Sunday, NBC reported, which was shortly after Bolt crossed the finish line ahead of Justin Gatlin.
Terminal 8 was evacuated as a precaution and flights briefly halted before a search established there was no danger.
“An official told NBC News that cheering, clapping and banging from people watching the Olympic Games may have been misinterpreted as a fight and gunshots,” the report said.
New York Police Department Special Operations Division Chief Harry Wedin said earlier that Port Authority, NYPD and Emergency Service Unit police were clearing Terminal 1 and Terminal 8.
But a pilot on a plane awaiting departure at Terminal 2 said police were sweeping that terminal after it was evacuated.
At Terminal 1, an AFP journalist was among passengers stranded on a plane on the tarmac for an hour and a half.
After deplaning, hundreds of people queuing to pass through immigration checkpoints were stuck in the area for more than two hours under heavy police presence.
Panic spread quickly through the crowd as police ordered people to lie on the ground, then evacuated them outside on the tarmac before making them pass through a corridor.
“Get down on the ground!” police officers yelled. “Move, move move!”
Police prohibited travellers from making phone calls or taking photographs. One man was arrested for trying to capture images of the chaotic scenes.
When the travellers returned to the immigration area, there was renewed panic as armed police ran back and forth. Some travellers were ordered to hide in immigration booths. Police gave travellers no explanation for the security incident.
One woman sobbed loudly because she lost her nine-year-old child in the commotion.
Bolt timed 9.81sec to become the first athlete to win the Olympic 100m three times in a row.