New York Police Department spokesman Paul Browne said a worker on the bridge that connects the New York City boroughs of Manhattan, Queens and the Bronx found the vehicle apparently smelling of gas.
Witnesses say they saw a dark skinned male, wearing dark clothing and carrying a white bag fleeing from the vehicle.
When officials first checked the vehicle, they say the keys were still in the ignition.
Police say the bomb squad and Hazmat teams cut a hole in the side of the moving van and found nothing inside.
The bridge was slowly beginning to reopen around 12:30am Thursday morning.
Officials towed the vehicle away to fully examine it.