Crew aboard a "shinkansen" bullet train reported a burning smell and strange noises when it pulled out of a station in southern Japan on Monday.
The train stopped for checks at Nagoya station in central Japan and inspectors discovered a crack in the chassis under one carriage as well as an oil leak.
If the train had continued to run, the crack could have caused it to derail in the worst-case scenario, transport officials said.
About 1,000 passengers aboard were unhurt and they continued their journey on fresh trains.
"We recognise it as a 'serious incident' as it was an extraordinary case... It could have led to an accident," said an official at the Japan Transport Safety Board.
It is the first such "serious incident" since the predecessor to the safety board was created in 2001, she said.
"We have sent three inspectors (to Nagoya) to find out the cause. Their report will include measures to prevent a recurrence," said the official, who declined to be named.
Japanese shinkansens have been derailed before due to earthquakes but no-one has been hurt.
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