The Meteorological Agency lifted the last emergency alerts for heavy rain in the Hokkaido cities of Sapporo, Chitose and Tomakomai on Thursday afternoon following earlier rainfall in excess of 80 mm per hour across much of the north.
The agency had earlier called for a "maximum" alert in anticipation of mudslides and overflowing rivers across the entire Ishikari region, which includes the prefectural capital of Sapporo, and parts of the adjacent Sorachi and Iburi regions.
The agency also issued evacuation advisories in areas including Sapporo and Iwamizawa, affecting 900,000 people in about 45,000 households.
Prime Minister Shinzo Abe instructed a task force at the Cabinet Office's crisis management center to do its "utmost" to help carry out evacuation plans.
Radar registered rainfall of 110 mm per hour in Tomakomai, while 100 mm per hour was registered in the cities of Eniwa and Chitose.
Sapporo set up a disaster management office on Wednesday morning, and issued an evacuation advisory to 700,000 residents in 330,000 households as a precaution against floods and mudslides.