Authorities announced a revised, higher death toll on Tuesday after search and rescue crews located the bodies of two more people. Six others are still reported missing.
Typhoon Dujuan left at least four people dead and 22 injured in Japan, while thousands of houses near Tokyo were without power after the storm swept through the region, authorities said on Tuesday.
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Officials warned that the death toll may continue to rise as six people remain missing, noting that search and rescue operations were underway to locate them.
The typhoon moved away from Japan's coast and out into the Pacific by the morning, allowing authorities to lift or downgrade most heavy rain and landslide warnings.
Dujuan had already led to the early closure in the capital of one of the world's biggest video game trade fairs.
Japan often sees strong typhoons in the late summer and early autumn, with other storms this season disrupting some events at the Asian Games being held in the country.
The Fire and Disaster Management Agency said three people died in Chiba prefecture and one in Kanagawa region, both near the capital, Tokyo.
Entire areas were completely submerged by floodwaters, causing considerable damage and bringing many critical services, major roads and public transportation to a standstill.
More than 45,000 households in Chiba near Tokyo were still without electricity on Tuesday afternoon, while over 460 houses suffered varying degrees of damage.
Although Dujuan weakened as it moved northeast, it dumped record rainfall in parts of the Tokyo area.
Oshima, an island about 120 kilometres south of central Tokyo, recorded 832 millimetres of rain over a 48-hour period, more than double its average rainfall for the whole of September, public broadcaster NHK reported.
Rainfall in Tokyo's Edogawa Ward reached a record 282.5 millimetres over 24 hours.
Scientists say human-driven climate change is intensifying the risk posed by heavy rains because a warmer atmosphere holds more water.