The Telegraph: The red and black snake, measuring three feet in length, was discovered by a surprised conductor shortly before 9am on board the Kodama 642 bullet train just outside Kyoto in Shiga prefecture.
Staff immediately halted the train before a worker from a nearby animal protection centre was sent to the scene to remove the snake from the seat.
The reptile is currently being treated as lost property by police, who suspect it may be the escaped pet of a rail passenger. They are currently searching for its owner.
None of the 200 passengers on board the halted bullet train was injured, according to the operator Central Japan Railway Co.
The animal is believed to be a Honduran milk snake, which is commonly bred in captivity and has become a popular pet choice due to its distinct colouring.
Bullet train operators normally request that passengers do not bring animals other than small birds of fish in containers on board their vehicles.
Halting a bullet train is a rare occurrence in Japan. Delays are usually the result of a major incident such as an earthquake or a suicide and often resulting in significant news coverage.