Even small delays in Japan's much-vaunted bullet trains are rare, and more unusual still are snakes on board holding up the speedy "shinkansen" services.

On Tuesday evening, a passenger alerted security to a 40-centimetre serpent lurking on a train between Nagoya and Tokyo, resulting in a 17-minute hold-up.

It was unclear whether the cold-blooded commuter was venomous or how it ended up on the train, and there was no injury or panic among passengers, a spokesman for Central Japan Railway Company said.

Shinkansen customers can bring small dogs, cats and other animals, including pigeons on board – but not snakes.

"It's difficult to imagine wild snakes somehow climbing onto the train at one of the stations. We have rules against bringing snakes into the shinkansen," the spokesman said.

"But we don't check passengers' baggage," he added.

The train was originally scheduled to go on to Osaka, but the company decided to use a different train for the trip, causing a delay of about 17 minutes, he said.

Patrols by uniformed security guards onboard bullet trains were scaled up after a fatal stabbing in 2018 on a shinkansen that shocked normally ultra-safe Japan.

Additional security was added for the Olympics in 2021 and Group of Seven meetings last year. (AFP)