Following a tip off, police personnel intercepted the bus near Samuktala and asked the passengers to get down.
On thorough search the explosive was found under a seat in an unclaimed bag last mid night, a police officer said.
The passenger, who had occupied the seat, was arrested and the driver and helper of the bus, which was plying on Alipurduar-Samuktala route, were detained for interrogation by the police.
Police were investigating if the explosive was meant for any militant group. The area is not very far from Bhutan border.