Haishen brought hurricane-like winds to wide swathes of Kyushu along with torrential downpours, storms surges, flooding and landslides, they added.
Two of those missing are believed to be Vietnamese trainees who work at a local construction company, local media said.
Of the more than 100 people injured, while many of them were in Kyushu, the powerful storm also caused a number of injuries to people in the Kinki and Chugoku regions, authorities said.
Kyushu Railway Co. said it is planning to restart its Shinkansen bullet train services on Tuesday in areas where it has been confirmed that they can operate safely.
They were all temporarily suspended due to the typhoon.
West Japan Railway Co. also suspended its Sanyo Shinkansen bullet train services between Hiroshima and Hakata and Tokaido Shinkansen bullet train services were temporarily suspended as well due to the typhoon, Central Japan Railway Co. said.
The severity of the typhoon also forced domestic flights in Kyushu to be grounded, according to operators.
Communication networks were also severely disrupted, with NTT Docomo Inc., KDDI Corp. and SoftBank Corp. saying their networks were affected not just in Kyushu, but also in Shikoku and Chugoku.
In the wake of the storm pummeling Kyushu before making landfall on the southeastern tip of the Korean Peninsula, where Typhoon Haishen has already claimed two lives in South Korea, according to local reports, the Japan Meteorological Agency (JMA) has still urged vigilance from people here for further torrential rain, strong winds and tidal surges in some areas.
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