The storm, packing maximum wind speeds of 72 kph (45 mph), is expected to move towards the Sea of Japan.
The Japan Meteorological Agency warned of risks from mudslides and floods after record-breaking rainfall over the last two days in some cities of the region.
The government will do its best to tackle the situation, Prime Minister Fumio Kishida told reporters. "We'll continue to provide information to residents and support those evacuating," he said.
Although Japan is observing a holiday, some high-speed bullet trains and regular services have been suspended in Iwate and other northern areas, while Japan Airlines and All Nippon Airways also cancelled flights with the affected regions.
Public broadcaster NHK said municipal authorities urged people in Iwate to take shelter. Media said no casualties had been reported, however.
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