JR West told AFP it has no plans to alter the exercise despite complaints from some employees.
About 190 staff working on safety maintenance for Japan's famed shinkansen bullet train have undergone the training, a company spokesman said.
"The training aims to teach our maintenance staff the importance of every part of their jobs," he told AFP.
"We pay close attention to safety while doing the training," he added, while acknowledging complaints from some staff members.
"We will continue this training while ensuring it serves a purpose and is done safely."
JR West introduced the training in 2016 after an accident in August 2015 in which part of the bullet train's exterior fell off, the spokesman said.
The purpose of the drill was reportedly to impress on the staff how fast the train moved and therefore how seriously they needed to take their jobs.
But it has proved unpopular with some employees, local media reported.
"It was a horrible experience," the Tokyo Shimbun newspaper quoted one employee as saying.
Another described the experience as "just like a public flogging," the Mainichi daily reported.
Japan's ultra-efficient shinkansen train network connects cities along the length and breadth of the country.
Despite the huge volume of passengers it serves, the network operates with an enviable punctuality rate. It also has an unparalleled safety record, with no one ever having been killed in a crash in its half-century of service.