Heavy rains early Thursday inundated the Nagoya Municipal Subway area in Nagoya Station, paralyzing services on the Higashiyama Line.
The floodwater reached the station, located in Nakamura Ward, at around 3 a.m., leaving subway tracks and the area near the entrance gates flooded.
Services on several stretches of the Higashiyama Line were suspended.
According to local transportation officials and firefighters, the floodwater was knee-deep in some parts of Nagoya Station's first basement level. They speculated the water may have reached the station through an air-supplying window connected to the station's machinery room, and that the fire department will pursue an investigation.
Although the floodwater had been pumped out of the station by 6 a.m., trains still had to wait for safety inspections on the electrical system along the tracks.
The service disruption left the station crowded with people who had to find other ways to get to school or work.
"I left home earlier than usual since the rain was heavy in the morning," said a 50-year-old office worker from Nishi Ward, adding before rushing off, "I think I'll manage to get to work on time."
The water also reached a subway station convenience store.
"We need to first sort out all the flood-damaged products," said a female worker who started cleaning up the flooding after arriving at the store at around 7 a.m.
According to the Nagoya District Meteorological Observatory, rainfall of up to 30.5 mm per hour was recorded within the city in the early hours of Thursday.
Nagoya was also hit by heavy rainfall in September 2013, when torrential rain led to severe flooding across the city. Some major roads were left under water. Sakae Station in the heart of Naka Ward was hit particularly hard, with water flooding the station and an adjacent underpass.