At least two people were killed and 47 others injured as typhoon Noru lashed through Japan's Honshu island before moving in a northeasterly direction on Tuesday morning, the weather agency said.
The typhoon, travelling at a speed of 25 km per hour, brought heavy rains to large regions of the island, according to the Japan Meteorological Agency (JMA).
Noru made landfall in Wakayama prefecture on Monday and carved a path through the Kinki and Hokuriku regions before moving slowly out to sea, reports Xinhua news agency.
The storm prompted evacuation orders affecting thousands of people and transportation networks were severely disrupted across the country.
As of 7.50 a.m. (local time) Tuesday, the storm was estimated to be passing through Niigata prefecture and moving north-northeast at a speed of 25 km per hour, the weather agency said.
It had a central atmospheric pressure of 986 hectopascals and was packing winds of up to 108 km per hour, the agency said.
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Landslide and flood alerts are still in place.
On Monday, Noru, the fifth typhoon of the season caused 450 domestic flights to be grounded, with airlines cancelling 26 flights as of Tuesday morning.